From a8f8916f58e139049c476ebaf3ca6c2c89ba1d78 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 07:19:53 +0100
Subject: [PATCH 1/9] cleaned up cli calling

---
 .gitignore                         |     4 +
 .idea/.gitignore                   |     3 -
 .idea/dictionaries/kevin.xml       | 30190 ---------------------------
 .idea/libraries/R_User_Library.xml |     6 -
 .idea/misc.xml                     |    10 -
 .idea/modules.xml                  |     8 -
 .idea/scaden.iml                   |    13 -
 .idea/vcs.xml                      |     6 -
 conda.recipe/meta.yaml             |    55 -
 environment.yml                    |     2 +-
 scaden/__init__.py                 |     3 +
 scaden/__main__.py                 |   145 +-
 scaden/cli.py                      |   138 -
 scripts/scaden                     |    14 -
 setup.py                           |     2 +-
 15 files changed, 153 insertions(+), 30446 deletions(-)
 delete mode 100644 .idea/.gitignore
 delete mode 100644 .idea/dictionaries/kevin.xml
 delete mode 100644 .idea/libraries/R_User_Library.xml
 delete mode 100644 .idea/misc.xml
 delete mode 100644 .idea/modules.xml
 delete mode 100644 .idea/scaden.iml
 delete mode 100644 .idea/vcs.xml
 delete mode 100644 conda.recipe/meta.yaml
 delete mode 100644 scaden/cli.py
 delete mode 100755 scripts/scaden

diff --git a/.gitignore b/.gitignore
index c0c219b..eda44ab 100644
--- a/.gitignore
+++ b/.gitignore
@@ -122,3 +122,7 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# extra
+.idea
+scaden.egg-info
\ No newline at end of file
diff --git a/.idea/.gitignore b/.idea/.gitignore
deleted file mode 100644
index 0e40fe8..0000000
--- a/.idea/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-
-# Default ignored files
-/workspace.xml
\ No newline at end of file
diff --git a/.idea/dictionaries/kevin.xml b/.idea/dictionaries/kevin.xml
deleted file mode 100644
index 01ac3b1..0000000
--- a/.idea/dictionaries/kevin.xml
+++ /dev/null
@@ -1,30190 +0,0 @@
-<component name="ProjectDictionaryState">
-  <dictionary name="kevin">
-    <words>
-      <w>.</w>
-      <w>...elt</w>
-      <w>...length</w>
-      <w>..2dge</w>
-      <w>..getNamespace</w>
-      <w>..stacktraceoff..</w>
-      <w>..stacktraceon..</w>
-      <w>.ArgsEnv</w>
-      <w>.AutoloadEnv</w>
-      <w>.BY</w>
-      <w>.BaseNamespaceEnv</w>
-      <w>.C</w>
-      <w>.C2nC</w>
-      <w>.C64</w>
-      <w>.C_R_addTaskCallback</w>
-      <w>.C_R_getTaskCallbackNames</w>
-      <w>.C_R_removeTaskCallback</w>
-      <w>.Call</w>
-      <w>.Call.graphics</w>
-      <w>.Call2</w>
-      <w>.Defunct</w>
-      <w>.Deprecated</w>
-      <w>.Device</w>
-      <w>.Devices</w>
-      <w>.DollarNames</w>
-      <w>.DollarNames.GRanges</w>
-      <w>.DollarNames.GenomicRanges</w>
-      <w>.DollarNames.Hub</w>
-      <w>.DollarNames.RangedSummarizedExperiment</w>
-      <w>.DollarNames.SummarizedExperiment</w>
-      <w>.EACHI</w>
-      <w>.EmptyPrimitiveSkeletons</w>
-      <w>.External</w>
-      <w>.External.graphics</w>
-      <w>.External2</w>
-      <w>.F_dchdc</w>
-      <w>.F_dqrcf</w>
-      <w>.F_dqrdc2</w>
-      <w>.F_dqrqty</w>
-      <w>.F_dqrqy</w>
-      <w>.F_dqrrsd</w>
-      <w>.F_dqrxb</w>
-      <w>.F_dtrco</w>
-      <w>.First.sys</w>
-      <w>.Fortran</w>
-      <w>.GRP</w>
-      <w>.GenericArgsEnv</w>
-      <w>.GlobalEnv</w>
-      <w>.Hub</w>
-      <w>.I</w>
-      <w>.Internal</w>
-      <w>.JULIAN</w>
-      <w>.Last.lib</w>
-      <w>.Last.value</w>
-      <w>.Library</w>
-      <w>.Library.site</w>
-      <w>.MCDcnp2</w>
-      <w>.MCDcnp2.rew</w>
-      <w>.MCDcons</w>
-      <w>.MCDsingularityMsg</w>
-      <w>.MFclass</w>
-      <w>.Machine</w>
-      <w>.Mchi</w>
-      <w>.Mchi.tuning.default</w>
-      <w>.Mchi.tuning.defaults</w>
-      <w>.Mpsi</w>
-      <w>.Mpsi.tuning.default</w>
-      <w>.Mpsi.tuning.defaults</w>
-      <w>.MrhoInf</w>
-      <w>.Mwgt</w>
-      <w>.Mwgt.psi1</w>
-      <w>.N</w>
-      <w>.NotYetImplemented</w>
-      <w>.NotYetUsed</w>
-      <w>.OldClassesList</w>
-      <w>.OptRequireMethods</w>
-      <w>.Options</w>
-      <w>.POSIXct</w>
-      <w>.POSIXlt</w>
-      <w>.Platform</w>
-      <w>.PlotPhyloEnv</w>
-      <w>.Primitive</w>
-      <w>.RtangleCodeLabel</w>
-      <w>.S3PrimitiveGenerics</w>
-      <w>.S3methods</w>
-      <w>.S4methods</w>
-      <w>.SD</w>
-      <w>.SQL92Keywords</w>
-      <w>.Script</w>
-      <w>.ShortPrimitiveSkeletons</w>
-      <w>.SuiteSparse_version</w>
-      <w>.T2Cmat</w>
-      <w>.TAOCP1997init</w>
-      <w>.Tcl</w>
-      <w>.Tcl.args</w>
-      <w>.Tcl.args.objv</w>
-      <w>.Tcl.callback</w>
-      <w>.Tcl.objv</w>
-      <w>.Tk.ID</w>
-      <w>.Tk.newwin</w>
-      <w>.Tk.subwin</w>
-      <w>.TkRoot</w>
-      <w>.TkUp</w>
-      <w>.TraceWithMethods</w>
-      <w>.__C__.NULL</w>
-      <w>.__C__.Other</w>
-      <w>.__C__.QA</w>
-      <w>.__C__.QA2</w>
-      <w>.__C__.Roche</w>
-      <w>.__C__.SRUtil</w>
-      <w>.__C__.ShortReadBase</w>
-      <w>.__C__.Solexa</w>
-      <w>.__C__.environment</w>
-      <w>.__C__.externalptr</w>
-      <w>.__C__.name</w>
-      <w>.__C__AAMultipleAlignment</w>
-      <w>.__C__AAString</w>
-      <w>.__C__AAStringSet</w>
-      <w>.__C__AAStringSetList</w>
-      <w>.__C__ACtree2</w>
-      <w>.__C__ANY</w>
-      <w>.__C__AffyBatch</w>
-      <w>.__C__AffyDatPkg</w>
-      <w>.__C__AgEdge</w>
-      <w>.__C__AgNode</w>
-      <w>.__C__AgTextLabel</w>
-      <w>.__C__AgiAnnDbMap</w>
-      <w>.__C__AlignedDataFrame</w>
-      <w>.__C__AlignedRead</w>
-      <w>.__C__AlignedReadTrack</w>
-      <w>.__C__AlignedXStringSet</w>
-      <w>.__C__AlignedXStringSet0</w>
-      <w>.__C__AlignmentsTrack</w>
-      <w>.__C__AllVariants</w>
-      <w>.__C__AnchorSet</w>
-      <w>.__C__AnnDbBimap</w>
-      <w>.__C__AnnDbMap</w>
-      <w>.__C__AnnDbObj</w>
-      <w>.__C__AnnDbPkgSeed</w>
-      <w>.__C__AnnObj</w>
-      <w>.__C__Annotated</w>
-      <w>.__C__AnnotatedDataFrame</w>
-      <w>.__C__AnnotationDb</w>
-      <w>.__C__AnnotationFilter</w>
-      <w>.__C__AnnotationFilterList</w>
-      <w>.__C__AnnotationHub</w>
-      <w>.__C__AnnotationHubResource</w>
-      <w>.__C__AnnotationIdentifier</w>
-      <w>.__C__AnnotationTrack</w>
-      <w>.__C__ApplyPileupsParam</w>
-      <w>.__C__Array</w>
-      <w>.__C__ArrayArbitraryGrid</w>
-      <w>.__C__ArrayGrid</w>
-      <w>.__C__ArrayIntensity</w>
-      <w>.__C__ArrayRegularGrid</w>
-      <w>.__C__ArrayViewport</w>
-      <w>.__C__AsIs</w>
-      <w>.__C__Assay</w>
-      <w>.__C__AssayData</w>
-      <w>.__C__Assays</w>
-      <w>.__C__AtomicList</w>
-      <w>.__C__AutoEncoder</w>
-      <w>.__C__Axt</w>
-      <w>.__C__BED15File</w>
-      <w>.__C__BEDFile</w>
-      <w>.__C__BEDGraphFile</w>
-      <w>.__C__BEDPEFile</w>
-      <w>.__C__BSgenome</w>
-      <w>.__C__BSgenomeDataPkgSeed</w>
-      <w>.__C__BSgenomeViews</w>
-      <w>.__C__BSseq</w>
-      <w>.__C__BSseqStat</w>
-      <w>.__C__BSseqTstat</w>
-      <w>.__C__BString</w>
-      <w>.__C__BStringSet</w>
-      <w>.__C__BStringSetList</w>
-      <w>.__C__BamFile</w>
-      <w>.__C__BamFileList</w>
-      <w>.__C__BamSampler</w>
-      <w>.__C__BamViews</w>
-      <w>.__C__BasicRaster</w>
-      <w>.__C__BasicTrackLine</w>
-      <w>.__C__BatchJobsParam</w>
-      <w>.__C__BcfFile</w>
-      <w>.__C__BcfFileList</w>
-      <w>.__C__BeadLevelList</w>
-      <w>.__C__Bed15TrackLine</w>
-      <w>.__C__BezierCurve</w>
-      <w>.__C__BigWigFile</w>
-      <w>.__C__BigWigFileList</w>
-      <w>.__C__BigWigSelection</w>
-      <w>.__C__Bimap</w>
-      <w>.__C__BiocParallelParam</w>
-      <w>.__C__BiomartGeneRegionTrack</w>
-      <w>.__C__BowtieQA</w>
-      <w>.__C__BroadCollection</w>
-      <w>.__C__BrowserSession</w>
-      <w>.__C__BrowserView</w>
-      <w>.__C__BrowserViewList</w>
-      <w>.__C__BunchKaufman</w>
-      <w>.__C__ByPos_MIndex</w>
-      <w>.__C__CAGEset</w>
-      <w>.__C__CFILE</w>
-      <w>.__C__CHMfactor</w>
-      <w>.__C__CHMsimpl</w>
-      <w>.__C__CHMsuper</w>
-      <w>.__C__CNE</w>
-      <w>.__C__CRS</w>
-      <w>.__C__CURLHandle</w>
-      <w>.__C__CdsEndFilter</w>
-      <w>.__C__CdsStartFilter</w>
-      <w>.__C__ChainFile</w>
-      <w>.__C__CharacterFilter</w>
-      <w>.__C__CharacterList</w>
-      <w>.__C__ChipDb</w>
-      <w>.__C__Cholesky</w>
-      <w>.__C__CholeskyFactorization</w>
-      <w>.__C__ChrBandTree</w>
-      <w>.__C__ChrCollection</w>
-      <w>.__C__ChrMapHyperGParams</w>
-      <w>.__C__ChrMapHyperGResult</w>
-      <w>.__C__ChrMapLinearMParams</w>
-      <w>.__C__ChrMapLinearMResult</w>
-      <w>.__C__ChrlocCollection</w>
-      <w>.__C__ChunkedRleArraySeed</w>
-      <w>.__C__ClassUnionRepresentation</w>
-      <w>.__C__CodingVariants</w>
-      <w>.__C__CollapsedVCF</w>
-      <w>.__C__CollectionIdType</w>
-      <w>.__C__CollectionType</w>
-      <w>.__C__ComplexList</w>
-      <w>.__C__CompressedAtomicList</w>
-      <w>.__C__CompressedCharacterList</w>
-      <w>.__C__CompressedComplexList</w>
-      <w>.__C__CompressedFactorList</w>
-      <w>.__C__CompressedFile</w>
-      <w>.__C__CompressedGrouping</w>
-      <w>.__C__CompressedIRangesList</w>
-      <w>.__C__CompressedIntegerList</w>
-      <w>.__C__CompressedList</w>
-      <w>.__C__CompressedLogicalList</w>
-      <w>.__C__CompressedManyToManyGrouping</w>
-      <w>.__C__CompressedManyToOneGrouping</w>
-      <w>.__C__CompressedNormalIRangesList</w>
-      <w>.__C__CompressedNumericList</w>
-      <w>.__C__CompressedRawList</w>
-      <w>.__C__CompressedRleList</w>
-      <w>.__C__CompressedSplitDataFrameList</w>
-      <w>.__C__CompressedVRangesList</w>
-      <w>.__C__ComputedCollection</w>
-      <w>.__C__Constraint</w>
-      <w>.__C__Constraint_OR_NULL</w>
-      <w>.__C__Cov</w>
-      <w>.__C__CovClassic</w>
-      <w>.__C__CovControl</w>
-      <w>.__C__CovControlMMest</w>
-      <w>.__C__CovControlMcd</w>
-      <w>.__C__CovControlMest</w>
-      <w>.__C__CovControlMrcd</w>
-      <w>.__C__CovControlMve</w>
-      <w>.__C__CovControlOgk</w>
-      <w>.__C__CovControlSde</w>
-      <w>.__C__CovControlSest</w>
-      <w>.__C__CovMMest</w>
-      <w>.__C__CovMcd</w>
-      <w>.__C__CovMest</w>
-      <w>.__C__CovMve</w>
-      <w>.__C__CovOgk</w>
-      <w>.__C__CovRobust</w>
-      <w>.__C__CovSde</w>
-      <w>.__C__CovSest</w>
-      <w>.__C__CsparseMatrix</w>
-      <w>.__C__CustomTrack</w>
-      <w>.__C__DBIConnection</w>
-      <w>.__C__DBIDriver</w>
-      <w>.__C__DBIObject</w>
-      <w>.__C__DBIResult</w>
-      <w>.__C__DESeqDataSet</w>
-      <w>.__C__DESeqResults</w>
-      <w>.__C__DESeqTransform</w>
-      <w>.__C__DGEExact</w>
-      <w>.__C__DGEGLM</w>
-      <w>.__C__DGELRT</w>
-      <w>.__C__DGEList</w>
-      <w>.__C__DMS</w>
-      <w>.__C__DNAMultipleAlignment</w>
-      <w>.__C__DNAString</w>
-      <w>.__C__DNAStringSet</w>
-      <w>.__C__DNAStringSetList</w>
-      <w>.__C__DOTerms</w>
-      <w>.__C__DOTermsAnnDbBimap</w>
-      <w>.__C__DRR</w>
-      <w>.__C__DatPkg</w>
-      <w>.__C__DataFrame</w>
-      <w>.__C__DataFrameList</w>
-      <w>.__C__DataTable</w>
-      <w>.__C__DataTable_OR_NULL</w>
-      <w>.__C__DataTrack</w>
-      <w>.__C__Date</w>
-      <w>.__C__DelayedArray</w>
-      <w>.__C__DelayedMatrix</w>
-      <w>.__C__DelegatingGenomicRanges</w>
-      <w>.__C__DetailsAnnotationTrack</w>
-      <w>.__C__DiffusionMaps</w>
-      <w>.__C__DimReduc</w>
-      <w>.__C__DisplayPars</w>
-      <w>.__C__DoparParam</w>
-      <w>.__C__DrL</w>
-      <w>.__C__Dups</w>
-      <w>.__C__Duration</w>
-      <w>.__C__EBAM</w>
-      <w>.__C__EBMTP</w>
-      <w>.__C__EList</w>
-      <w>.__C__EListRaw</w>
-      <w>.__C__ENSEMBLIdentifier</w>
-      <w>.__C__EmptyMethodsList</w>
-      <w>.__C__EnsDb</w>
-      <w>.__C__EntrezFilter</w>
-      <w>.__C__EntrezIdentifier</w>
-      <w>.__C__EnzymeIdentifier</w>
-      <w>.__C__ExonEndFilter</w>
-      <w>.__C__ExonIdFilter</w>
-      <w>.__C__ExonNameFilter</w>
-      <w>.__C__ExonRankFilter</w>
-      <w>.__C__ExonStartFilter</w>
-      <w>.__C__ExpandedVCF</w>
-      <w>.__C__Expanded_TB_PDict</w>
-      <w>.__C__ExperimentList</w>
-      <w>.__C__ExperimentPath</w>
-      <w>.__C__ExpressionSet</w>
-      <w>.__C__ExpressionSetCollection</w>
-      <w>.__C__ExpressionSetIllumina</w>
-      <w>.__C__Extent</w>
-      <w>.__C__ExternalReference</w>
-      <w>.__C__FLXM</w>
-      <w>.__C__FLXMC</w>
-      <w>.__C__FLXMR</w>
-      <w>.__C__FLXMRfix</w>
-      <w>.__C__FLXMRglm</w>
-      <w>.__C__FLXMRglmfix</w>
-      <w>.__C__FLXMRlmc</w>
-      <w>.__C__FLXMRlmcfix</w>
-      <w>.__C__FLXMRlmer</w>
-      <w>.__C__FLXMRlmm</w>
-      <w>.__C__FLXMRlmmc</w>
-      <w>.__C__FLXMRlmmcfix</w>
-      <w>.__C__FLXMRlmmfix</w>
-      <w>.__C__FLXMRmgcv</w>
-      <w>.__C__FLXMRrobglm</w>
-      <w>.__C__FLXMRziglm</w>
-      <w>.__C__FLXP</w>
-      <w>.__C__FLXPmultinom</w>
-      <w>.__C__FLXR</w>
-      <w>.__C__FLXRmstep</w>
-      <w>.__C__FLXRoptim</w>
-      <w>.__C__FLXcomponent</w>
-      <w>.__C__FLXcontrol</w>
-      <w>.__C__FLXdist</w>
-      <w>.__C__FLXnested</w>
-      <w>.__C__FaFile</w>
-      <w>.__C__FaFileList</w>
-      <w>.__C__FactorList</w>
-      <w>.__C__FastICA</w>
-      <w>.__C__FastaFile</w>
-      <w>.__C__FastqFile</w>
-      <w>.__C__FastqFileList</w>
-      <w>.__C__FastqFileReader</w>
-      <w>.__C__FastqQA</w>
-      <w>.__C__FastqQuality</w>
-      <w>.__C__FastqSampler</w>
-      <w>.__C__FastqSamplerList</w>
-      <w>.__C__FastqStreamer</w>
-      <w>.__C__FastqStreamerList</w>
-      <w>.__C__FeatureDb</w>
-      <w>.__C__FilterMatrix</w>
-      <w>.__C__FilterRules</w>
-      <w>.__C__FindA0</w>
-      <w>.__C__FiveUTRVariants</w>
-      <w>.__C__FlatBimap</w>
-      <w>.__C__FormattedInteger</w>
-      <w>.__C__FormattedNumber</w>
-      <w>.__C__FormulaParts</w>
-      <w>.__C__FramedHTMLPage</w>
-      <w>.__C__FruchtermanReingold</w>
-      <w>.__C__GAlignmentPairs</w>
-      <w>.__C__GAlignments</w>
-      <w>.__C__GAlignmentsList</w>
-      <w>.__C__GFF1File</w>
-      <w>.__C__GFF2File</w>
-      <w>.__C__GFF3File</w>
-      <w>.__C__GFFFile</w>
-      <w>.__C__GNCList</w>
-      <w>.__C__GOAllFrame</w>
-      <w>.__C__GOAllFrameIdentifier</w>
-      <w>.__C__GOCollection</w>
-      <w>.__C__GODb</w>
-      <w>.__C__GOFrame</w>
-      <w>.__C__GOHyperGParams</w>
-      <w>.__C__GOHyperGResult</w>
-      <w>.__C__GOSemSimDATA</w>
-      <w>.__C__GOTerms</w>
-      <w>.__C__GOTermsAnnDbBimap</w>
-      <w>.__C__GPos</w>
-      <w>.__C__GRangePairs</w>
-      <w>.__C__GRanges</w>
-      <w>.__C__GRangesFilter</w>
-      <w>.__C__GRangesList</w>
-      <w>.__C__GRanges_OR_NULL</w>
-      <w>.__C__GTFFile</w>
-      <w>.__C__GVFFile</w>
-      <w>.__C__GappedReads</w>
-      <w>.__C__GdObject</w>
-      <w>.__C__GeneBiotypeFilter</w>
-      <w>.__C__GeneColorSet</w>
-      <w>.__C__GeneEndFilter</w>
-      <w>.__C__GeneIdFilter</w>
-      <w>.__C__GeneIdentifierType</w>
-      <w>.__C__GeneRegionTrack</w>
-      <w>.__C__GeneSet</w>
-      <w>.__C__GeneSetCollection</w>
-      <w>.__C__GeneStartFilter</w>
-      <w>.__C__GenenameFilter</w>
-      <w>.__C__GenenameIdentifier</w>
-      <w>.__C__GenomeAxisTrack</w>
-      <w>.__C__GenomeDescription</w>
-      <w>.__C__GenomicMethylSet</w>
-      <w>.__C__GenomicRanges</w>
-      <w>.__C__GenomicRangesList</w>
-      <w>.__C__GenomicRanges_OR_GRangesList</w>
-      <w>.__C__GenomicRanges_OR_GenomicRangesList</w>
-      <w>.__C__GenomicRanges_OR_missing</w>
-      <w>.__C__GenomicRatioSet</w>
-      <w>.__C__Go3AnnDbBimap</w>
-      <w>.__C__GoAnnDbBimap</w>
-      <w>.__C__Graph</w>
-      <w>.__C__GraphTrackLine</w>
-      <w>.__C__GridTopology</w>
-      <w>.__C__GroupedIRanges</w>
-      <w>.__C__Grouping</w>
-      <w>.__C__GroupingIRanges</w>
-      <w>.__C__GroupingRanges</w>
-      <w>.__C__H2LGrouping</w>
-      <w>.__C__H5IdComponent</w>
-      <w>.__C__HDF5Array</w>
-      <w>.__C__HDF5ArraySeed</w>
-      <w>.__C__HDF5Matrix</w>
-      <w>.__C__HDF5RealizationSink</w>
-      <w>.__C__HLLE</w>
-      <w>.__C__HLS</w>
-      <w>.__C__HSV</w>
-      <w>.__C__HTMLInternalDocument</w>
-      <w>.__C__HTMLPage</w>
-      <w>.__C__HighlightTrack</w>
-      <w>.__C__Hits</w>
-      <w>.__C__HitsList</w>
-      <w>.__C__Hub</w>
-      <w>.__C__HyperGParams</w>
-      <w>.__C__HyperGResult</w>
-      <w>.__C__HyperGResultBase</w>
-      <w>.__C__IDate</w>
-      <w>.__C__INTERSECTset</w>
-      <w>.__C__IPos</w>
-      <w>.__C__IRanges</w>
-      <w>.__C__IRangesList</w>
-      <w>.__C__IRanges_OR_IPos</w>
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-      <w>.performance.expected.cost</w>
-      <w>.performance.f</w>
-      <w>.performance.false.negative.rate</w>
-      <w>.performance.false.positive.rate</w>
-      <w>.performance.lift</w>
-      <w>.performance.mean.cross.entropy</w>
-      <w>.performance.mutual.information</w>
-      <w>.performance.negative.predictive.value</w>
-      <w>.performance.odds.ratio</w>
-      <w>.performance.phi</w>
-      <w>.performance.plot.canvas</w>
-      <w>.performance.plot.horizontal.avg</w>
-      <w>.performance.plot.no.avg</w>
-      <w>.performance.plot.threshold.avg</w>
-      <w>.performance.plot.vertical.avg</w>
-      <w>.performance.positive.predictive.value</w>
-      <w>.performance.precision.recall.break.even.point</w>
-      <w>.performance.prediction.conditioned.fallout</w>
-      <w>.performance.prediction.conditioned.miss</w>
-      <w>.performance.rate.of.negative.predictions</w>
-      <w>.performance.rate.of.positive.predictions</w>
-      <w>.performance.rocconvexhull</w>
-      <w>.performance.root.mean.squared.error</w>
-      <w>.performance.sar</w>
-      <w>.performance.true.negative.rate</w>
-      <w>.performance.true.positive.rate</w>
-      <w>.plot.performance</w>
-      <w>.popath</w>
-      <w>.postForm</w>
-      <w>.preformat.ts</w>
-      <w>.primTrace</w>
-      <w>.primUntrace</w>
-      <w>.print.via.format</w>
-      <w>.psi.const</w>
-      <w>.psi.ggw.findc</w>
-      <w>.psi.lqq.findc</w>
-      <w>.psi2ipsi</w>
-      <w>.pt</w>
-      <w>.rbind.data.table</w>
-      <w>.readRDS</w>
-      <w>.regularize.Mpsi</w>
-      <w>.rmpkg</w>
-      <w>.romans</w>
-      <w>.rowMeans</w>
-      <w>.rowSums</w>
-      <w>.row_names_info</w>
-      <w>.runApp</w>
-      <w>.sarg</w>
-      <w>.saveRDS</w>
-      <w>.sdate</w>
-      <w>.sday.of.week</w>
-      <w>.select.args</w>
-      <w>.select.prefix</w>
-      <w>.selectSuperClasses</w>
-      <w>.setAffyOptions</w>
-      <w>.setRNG</w>
-      <w>.setUp</w>
-      <w>.set_row_names</w>
-      <w>.signalSimpleWarning</w>
-      <w>.signflip</w>
-      <w>.silenceF</w>
-      <w>.sjulian</w>
-      <w>.sleap.year</w>
-      <w>.slice.run</w>
-      <w>.slotNames</w>
-      <w>.solve.dgC.chol</w>
-      <w>.solve.dgC.lu</w>
-      <w>.solve.dgC.qr</w>
-      <w>.sparseDiagonal</w>
-      <w>.standard_regexps</w>
-      <w>.stroke</w>
-      <w>.subset</w>
-      <w>.subset2</w>
-      <w>.subsetByPython</w>
-      <w>.subsetBySpan</w>
-      <w>.subsetCode</w>
-      <w>.symDiagonal</w>
-      <w>.tearDown</w>
-      <w>.trDiagonal</w>
-      <w>.traceback</w>
-      <w>.transformAccession</w>
-      <w>.tryResumeInterrupt</w>
-      <w>.uncompressTipLabel</w>
-      <w>.undebugMethod</w>
-      <w>.untracedFunction</w>
-      <w>.updateCHMfactor</w>
-      <w>.userHooksEnv</w>
-      <w>.valid.factor</w>
-      <w>.validateCsparse</w>
-      <w>.valueClassTest</w>
-      <w>.wgtFUN.covComed</w>
-      <w>.wgtFUN.covMcd</w>
-      <w>.whichFormat</w>
-      <w>A1_to_R1C1</w>
-      <w>AAMultipleAlignment</w>
-      <w>AAString</w>
-      <w>AAStringSet</w>
-      <w>AAStringSetList</w>
-      <w>AA_ALPHABET</w>
-      <w>AA_PROTEINOGENIC</w>
-      <w>AA_STANDARD</w>
-      <w>AAsubst</w>
-      <w>ABH.h0</w>
-      <w>ACC2homology</w>
-      <w>ACCNUMStats</w>
-      <w>ACF</w>
-      <w>AES</w>
-      <w>AIC</w>
-      <w>AIC.nlrq</w>
-      <w>AIC.rq</w>
-      <w>AIC.rqs</w>
-      <w>AIC.rqss</w>
-      <w>ALL</w>
-      <w>ALRAChooseKPlot</w>
-      <w>AMINO_ACID_CODE</w>
-      <w>AMSsurvey</w>
-      <w>AMUSE</w>
-      <w>ANSI</w>
-      <w>API</w>
-      <w>ARMAacf</w>
-      <w>ARMAtoMA</w>
-      <w>ASCII</w>
-      <w>ASCII.BEL</w>
-      <w>ASCII.BS</w>
-      <w>ASCII.CR</w>
-      <w>ASCII.DC1</w>
-      <w>ASCII.DC3</w>
-      <w>ASCII.ESC</w>
-      <w>ASCII.FF</w>
-      <w>ASCII.HT</w>
-      <w>ASCII.LF</w>
-      <w>ASCII.SI</w>
-      <w>ASCII.SO</w>
-      <w>ASCIIfy</w>
-      <w>AST</w>
-      <w>AUC</w>
-      <w>AUC_lnK_R_NX</w>
-      <w>AUCi</w>
-      <w>AUTH_ANY</w>
-      <w>AUTH_ANYSAFE</w>
-      <w>AUTH_BASIC</w>
-      <w>AUTH_DIGEST</w>
-      <w>AUTH_DIGEST_IE</w>
-      <w>AUTH_GSSNEGOTIATE</w>
-      <w>AUTH_NONE</w>
-      <w>AUTH_NTLM</w>
-      <w>AUTH_NTLM_WB</w>
-      <w>AUTH_ONLY</w>
-      <w>Abidjan</w>
-      <w>Accession</w>
-      <w>Accra</w>
-      <w>AccumulateCallback</w>
-      <w>Adak</w>
-      <w>AddMetaData</w>
-      <w>AddModuleScore</w>
-      <w>Addis_Ababa</w>
-      <w>Adelaide</w>
-      <w>Aden</w>
-      <w>Adler</w>
-      <w>Adobe_glyphs</w>
-      <w>Advent1st</w>
-      <w>Advent2nd</w>
-      <w>Advent3rd</w>
-      <w>Advent4th</w>
-      <w>AffyRNAdeg</w>
-      <w>AgEdge</w>
-      <w>AgNode</w>
-      <w>Aggregate</w>
-      <w>Aids2</w>
-      <w>AirPassengers</w>
-      <w>Alfalfa</w>
-      <w>Algiers</w>
-      <w>AlignedDataFrame</w>
-      <w>AlignedRead</w>
-      <w>AlignedReadTrack</w>
-      <w>AlignmentsTrack</w>
-      <w>AllButCelsForReadAffy</w>
-      <w>AllSaints</w>
-      <w>AllSouls</w>
-      <w>AllVariants</w>
-      <w>Almaty</w>
-      <w>Amman</w>
-      <w>Amsterdam</w>
-      <w>Anadyr</w>
-      <w>Anchorage</w>
-      <w>Andorra</w>
-      <w>Angell</w>
-      <w>Anguilla</w>
-      <w>Animals</w>
-      <w>Animals2</w>
-      <w>Anno450K</w>
-      <w>AnnoEPIC</w>
-      <w>AnnoOrEntrezIdentifier</w>
-      <w>AnnotatedDataFrame</w>
-      <w>AnnotationDbi</w>
-      <w>AnnotationFilter</w>
-      <w>AnnotationFilterList</w>
-      <w>AnnotationForge</w>
-      <w>AnnotationHub</w>
-      <w>AnnotationIdentifier</w>
-      <w>AnnotationTrack</w>
-      <w>Annunciation</w>
-      <w>Anova</w>
-      <w>Anscombe</w>
-      <w>Antananarivo</w>
-      <w>Antigua</w>
-      <w>AovSum</w>
-      <w>Apia</w>
-      <w>Appalachia</w>
-      <w>ApplyPileupsParam</w>
-      <w>Aqtau</w>
-      <w>Aqtobe</w>
-      <w>Araguaina</w>
-      <w>ArcObj2SLDF</w>
-      <w>Arg</w>
-      <w>Args</w>
-      <w>Arguments</w>
-      <w>Arith</w>
-      <w>ArrayArbitraryGrid</w>
-      <w>ArrayIntensity</w>
-      <w>ArrayRegularGrid</w>
-      <w>ArrayViewport</w>
-      <w>ArrayWeights</w>
-      <w>Arrests</w>
-      <w>Aruba</w>
-      <w>As.mcmc.list</w>
-      <w>Ascension</w>
-      <w>AsciiToInt</w>
-      <w>AshWednesday</w>
-      <w>Ashgabat</w>
-      <w>Asmara</w>
-      <w>Assay</w>
-      <w>Assays</w>
-      <w>Assert</w>
-      <w>AssumptionOfMary</w>
-      <w>Asuncion</w>
-      <w>Asymbound</w>
-      <w>AsympH0</w>
-      <w>Async</w>
-      <w>AsyncVaried</w>
-      <w>Athens</w>
-      <w>Atikokan</w>
-      <w>Auckland</w>
-      <w>AugmentPlot</w>
-      <w>AutoEncoder</w>
-      <w>AverageExpression</w>
-      <w>Axis</w>
-      <w>AxisSecondary</w>
-      <w>Axt</w>
-      <w>Azores</w>
-      <w>BASH</w>
-      <w>BASHCompact</w>
-      <w>BASHDiffuse</w>
-      <w>BASHExtended</w>
-      <w>BBmisc</w>
-      <w>BD</w>
-      <w>BED15File</w>
-      <w>BEDFile</w>
-      <w>BEDGraphFile</w>
-      <w>BEDPEFile</w>
-      <w>BEPS</w>
-      <w>BH</w>
-      <w>BIC</w>
-      <w>BJsales</w>
-      <w>BLOSUM100</w>
-      <w>BLOSUM45</w>
-      <w>BLOSUM50</w>
-      <w>BLOSUM62</w>
-      <w>BLOSUM80</w>
-      <w>BMIQ</w>
-      <w>BOD</w>
-      <w>BOTHlabels</w>
-      <w>BROWSE</w>
-      <w>BS.chr22</w>
-      <w>BSgenome</w>
-      <w>BSgenome.Hsapiens.UCSC.hg19</w>
-      <w>BSgenome.Hsapiens.UCSC.hg38</w>
-      <w>BSgenomeViews</w>
-      <w>BSmooth</w>
-      <w>BSmooth.tstat</w>
-      <w>BSseq</w>
-      <w>BSseqStat</w>
-      <w>BSseqTstat</w>
-      <w>BString</w>
-      <w>BStringSet</w>
-      <w>BStringSetList</w>
-      <w>BTC</w>
-      <w>BTY</w>
-      <w>BYlogreg</w>
-      <w>Baghdad</w>
-      <w>Bahia</w>
-      <w>Bahrain</w>
-      <w>Baku</w>
-      <w>BamFile</w>
-      <w>BamFileList</w>
-      <w>BamSampler</w>
-      <w>BamViews</w>
-      <w>Bamako</w>
-      <w>Bangkok</w>
-      <w>Bangui</w>
-      <w>Banjul</w>
-      <w>Barbados</w>
-      <w>BarcodeInflectionsPlot</w>
-      <w>BasicObject</w>
-      <w>BatchJobs</w>
-      <w>BatchJobsParam</w>
-      <w>Baumann</w>
-      <w>BayesFactor</w>
-      <w>BcfFile</w>
-      <w>BcfFileList</w>
-      <w>Bdists</w>
-      <w>BeadDataPackR</w>
-      <w>Bechtoldt</w>
-      <w>Bechtoldt.1</w>
-      <w>Bechtoldt.2</w>
-      <w>Beirut</w>
-      <w>Belem</w>
-      <w>Belgrade</w>
-      <w>Belize</w>
-      <w>Berlin</w>
-      <w>Bermuda</w>
-      <w>Beta2M</w>
-      <w>Bfox</w>
-      <w>BiasedUrn</w>
-      <w>BigWigFile</w>
-      <w>BigWigFileList</w>
-      <w>BigWigSelection</w>
-      <w>Biobase</w>
-      <w>BiocGenerics</w>
-      <w>BiocInstaller</w>
-      <w>BiocParallel</w>
-      <w>BiomartGeneRegionTrack</w>
-      <w>Biostrings</w>
-      <w>BirthOfVirginMary</w>
-      <w>Bishkek</w>
-      <w>Bissau</w>
-      <w>Bk</w>
-      <w>Bk_permutations</w>
-      <w>Bk_plot</w>
-      <w>BlackAndWhite</w>
-      <w>Blackmore</w>
-      <w>Blantyre</w>
-      <w>Block.GUI</w>
-      <w>Blocks</w>
-      <w>BlueAndRed</w>
-      <w>Boa_Vista</w>
-      <w>BodyWeight</w>
-      <w>Bogota</w>
-      <w>Boise</w>
-      <w>BoldTitle</w>
-      <w>Boot</w>
-      <w>BootOneRefFreeEwasModel</w>
-      <w>BootRefFreeEwasModel</w>
-      <w>Bosco</w>
-      <w>Boston</w>
-      <w>Box.test</w>
-      <w>BoxCoxTrans</w>
-      <w>BoxingDay</w>
-      <w>Boxplot</w>
-      <w>Bratislava</w>
-      <w>Brazzaville</w>
-      <w>BregFix</w>
-      <w>Brisbane</w>
-      <w>BroadCollection</w>
-      <w>Broken_Hill</w>
-      <w>Brunei</w>
-      <w>Brussels</w>
-      <w>Bucharest</w>
-      <w>Budapest</w>
-      <w>BuenosAires</w>
-      <w>Buenos_Aires</w>
-      <w>BuildClusterTree</w>
-      <w>Bujumbura</w>
-      <w>BulkFlu</w>
-      <w>BunchKaufman</w>
-      <w>Burt</w>
-      <w>By</w>
-      <w>C</w>
-      <w>C.Monatsname</w>
-      <w>C.Wochentag</w>
-      <w>C.Wochentagkurz</w>
-      <w>C.weekday</w>
-      <w>CA</w>
-      <w>CACanadaDay</w>
-      <w>CACivicProvincialHoliday</w>
-      <w>CADM.global</w>
-      <w>CADM.post</w>
-      <w>CAFamilyDay</w>
-      <w>CAGEr</w>
-      <w>CALabourDay</w>
-      <w>CAThanksgivingDay</w>
-      <w>CAVictoriaDay</w>
-      <w>CAex</w>
-      <w>CCmaps</w>
-      <w>CES11</w>
-      <w>CET</w>
-      <w>CFILE</w>
-      <w>CHAscension</w>
-      <w>CHBerchtoldsDay</w>
-      <w>CHConfederationDay</w>
-      <w>CHKnabenschiessen</w>
-      <w>CHSechselaeuten</w>
-      <w>CIDFont</w>
-      <w>CIGAR_OPS</w>
-      <w>CIcdfplot</w>
-      <w>CJ</w>
-      <w>CKME</w>
-      <w>CLIENT_COMPRESS</w>
-      <w>CLIENT_CONNECT_WITH_DB</w>
-      <w>CLIENT_FOUND_ROWS</w>
-      <w>CLIENT_IGNORE_SIGPIPE</w>
-      <w>CLIENT_IGNORE_SPACE</w>
-      <w>CLIENT_INTERACTIVE</w>
-      <w>CLIENT_LOCAL_FILES</w>
-      <w>CLIENT_LONG_FLAG</w>
-      <w>CLIENT_LONG_PASSWORD</w>
-      <w>CLIENT_MULTI_RESULTS</w>
-      <w>CLIENT_MULTI_STATEMENTS</w>
-      <w>CLIENT_NO_SCHEMA</w>
-      <w>CLIENT_ODBC</w>
-      <w>CLIENT_PROTOCOL_41</w>
-      <w>CLIENT_RESERVED</w>
-      <w>CLIENT_SECURE_CONNECTION</w>
-      <w>CLIENT_SSL</w>
-      <w>CLIENT_TRANSACTIONS</w>
-      <w>CLL_covariates</w>
-      <w>CLL_data</w>
-      <w>CNA</w>
-      <w>CNE</w>
-      <w>CNE12</w>
-      <w>CNE21</w>
-      <w>CNEDanRer10Hg38</w>
-      <w>CNEDensity</w>
-      <w>CNEFinal</w>
-      <w>CNEHg38DanRer10</w>
-      <w>CNEMerged</w>
-      <w>CNEr</w>
-      <w>CO2</w>
-      <w>CO2data</w>
-      <w>COGravity</w>
-      <w>COMPACT</w>
-      <w>CPM</w>
-      <w>CPPdata</w>
-      <w>CRAN</w>
-      <w>CRAN.packages</w>
-      <w>CRAN_check_details</w>
-      <w>CRAN_check_issues</w>
-      <w>CRAN_check_results</w>
-      <w>CRAN_memtest_notes</w>
-      <w>CRAN_package_db</w>
-      <w>CRS</w>
-      <w>CST</w>
-      <w>CTSSclusteringMethod</w>
-      <w>CTSScoordinates</w>
-      <w>CTSSnormalizedTpm</w>
-      <w>CTSStagCount</w>
-      <w>CV</w>
-      <w>CVST</w>
-      <w>CaGalt</w>
-      <w>CaRemembranceDay</w>
-      <w>Cairo</w>
-      <w>CalculateBarcodeInflections</w>
-      <w>Calcutta</w>
-      <w>Cambridge_Bay</w>
-      <w>Campo_Grande</w>
-      <w>CanPop</w>
-      <w>Canary</w>
-      <w>Cancun</w>
-      <w>Cape_Verde</w>
-      <w>Caracas</w>
-      <w>Cars93</w>
-      <w>Casablanca</w>
-      <w>Cascades</w>
-      <w>CaseMatch</w>
-      <w>Casey</w>
-      <w>Cassini</w>
-      <w>Catalan_elections</w>
-      <w>Catamarca</w>
-      <w>Category</w>
-      <w>Cayenne</w>
-      <w>Cayman</w>
-      <w>Cbind</w>
-      <w>CdsEndFilter</w>
-      <w>CdsStartFilter</w>
-      <w>Cefamandole</w>
-      <w>CelebrationOfHolyCross</w>
-      <w>CellCycleScoring</w>
-      <w>CellScatter</w>
-      <w>CellSelector</w>
-      <w>CellTypeMeans27K</w>
-      <w>CellTypeMeans450K</w>
-      <w>Cells</w>
-      <w>Center</w>
-      <w>Ceuta</w>
-      <w>ChAMP</w>
-      <w>ChAMPdata</w>
-      <w>ChIPseeker</w>
-      <w>Chagos</w>
-      <w>ChainFile</w>
-      <w>Chainlink</w>
-      <w>ChangeLog</w>
-      <w>CharacterList</w>
-      <w>Chatham</w>
-      <w>CheckBMIQ</w>
-      <w>Chicago</w>
-      <w>ChicagoO3</w>
-      <w>ChickEgg</w>
-      <w>ChickWeight</w>
-      <w>Chihuahua</w>
-      <w>Chile</w>
-      <w>Chirot</w>
-      <w>Chisinau</w>
-      <w>Choibalsan</w>
-      <w>Cholesky</w>
-      <w>Chongqing</w>
-      <w>ChrBandTreeFromGraph</w>
-      <w>ChrCollection</w>
-      <w>ChristTheKing</w>
-      <w>Christmas</w>
-      <w>ChristmasDay</w>
-      <w>ChristmasEve</w>
-      <w>ChrlocCollection</w>
-      <w>ChunkCallback</w>
-      <w>Class</w>
-      <w>ClassStat</w>
-      <w>CleanupReporter</w>
-      <w>ClientValue</w>
-      <w>ClusterFuture</w>
-      <w>CmdArgsFunction</w>
-      <w>Cmetric</w>
-      <w>CobarOre</w>
-      <w>Cocos</w>
-      <w>CodingVariants</w>
-      <w>CoefMat</w>
-      <w>CoefMat.multigroupfit</w>
-      <w>Col</w>
-      <w>CollapseSpeciesExpressionMatrix</w>
-      <w>Colombo</w>
-      <w>Columns</w>
-      <w>ComBat</w>
-      <w>Combine</w>
-      <w>CombinePlots</w>
-      <w>Command</w>
-      <w>ComonGAP</w>
-      <w>Comoro</w>
-      <w>Compare</w>
-      <w>Complex</w>
-      <w>ComplexList</w>
-      <w>ComputedCollection</w>
-      <w>Conakry</w>
-      <w>Confint</w>
-      <w>Conj</w>
-      <w>ConnCompLabel</w>
-      <w>ConsensusClusterPlus</w>
-      <w>ConstantFuture</w>
-      <w>ContinuousRange</w>
-      <w>ContourLines2SLDF</w>
-      <w>ContrastMatrix</w>
-      <w>ControlProbes450K</w>
-      <w>ControlProbesEPIC</w>
-      <w>ConvertMedUnits</w>
-      <w>Coord</w>
-      <w>CoordCartesian</w>
-      <w>CoordFixed</w>
-      <w>CoordFlip</w>
-      <w>CoordMap</w>
-      <w>CoordPolar</w>
-      <w>CoordQuickmap</w>
-      <w>CoordSf</w>
-      <w>CoordTrans</w>
-      <w>Copenhagen</w>
-      <w>Cordoba</w>
-      <w>CorpusChristi</w>
-      <w>Costa_Rica</w>
-      <w>Cov</w>
-      <w>CovClassic</w>
-      <w>CovControlMMest</w>
-      <w>CovControlMcd</w>
-      <w>CovControlMest</w>
-      <w>CovControlMrcd</w>
-      <w>CovControlMve</w>
-      <w>CovControlOgk</w>
-      <w>CovControlSde</w>
-      <w>CovControlSest</w>
-      <w>CovMMest</w>
-      <w>CovMcd</w>
-      <w>CovMest</w>
-      <w>CovMrcd</w>
-      <w>CovMve</w>
-      <w>CovOgk</w>
-      <w>CovRobust</w>
-      <w>CovSde</w>
-      <w>CovSest</w>
-      <w>Cowles</w>
-      <w>CpG.GUI</w>
-      <w>CpGs</w>
-      <w>CreateAssayObject</w>
-      <w>CreateDimReducObject</w>
-      <w>CreateGeneActivityMatrix</w>
-      <w>CreateSeuratObject</w>
-      <w>CrohnD</w>
-      <w>Cs</w>
-      <w>Cstack_info</w>
-      <w>Cuiaba</w>
-      <w>Curacao</w>
-      <w>CurlFeatureBits</w>
-      <w>CurlGlobalBits</w>
-      <w>CurlNetrc</w>
-      <w>Currie</w>
-      <w>Curv</w>
-      <w>Cushings</w>
-      <w>CustomDistance</w>
-      <w>CustomPalette</w>
-      <w>CustomTrack</w>
-      <w>Cy3.N</w>
-      <w>Cy5.N</w>
-      <w>D</w>
-      <w>D1D2</w>
-      <w>D1ss</w>
-      <w>D1tr</w>
-      <w>D2ss</w>
-      <w>DBI</w>
-      <w>DDT</w>
-      <w>DEACTIVATED</w>
-      <w>DEAscension</w>
-      <w>DEChristmasEve</w>
-      <w>DECorpusChristi</w>
-      <w>DEFAULT_CIRC_SEQS</w>
-      <w>DEGermanUnity</w>
-      <w>DELETE</w>
-      <w>DENewYearsEve</w>
-      <w>DESeq</w>
-      <w>DESeq2</w>
-      <w>DESeqDataSet</w>
-      <w>DESeqDataSetFromHTSeqCount</w>
-      <w>DESeqDataSetFromMatrix</w>
-      <w>DESeqDataSetFromTximport</w>
-      <w>DESeqResults</w>
-      <w>DESeqTransform</w>
-      <w>DEoptimR</w>
-      <w>DFS</w>
-      <w>DGEList</w>
-      <w>DGN_EXTID2PATHID</w>
-      <w>DGN_PATHID2EXTID</w>
-      <w>DGN_PATHID2NAME</w>
-      <w>DLBCL</w>
-      <w>DM</w>
-      <w>DMFA</w>
-      <w>DMLfit.multiFactor</w>
-      <w>DMLtest</w>
-      <w>DMLtest.multiFactor</w>
-      <w>DMP.GUI</w>
-      <w>DMR.GUI</w>
-      <w>DMR.plot</w>
-      <w>DMRcate</w>
-      <w>DMRcatedata</w>
-      <w>DNAMultipleAlignment</w>
-      <w>DNAString</w>
-      <w>DNAStringSet</w>
-      <w>DNAStringSetList</w>
-      <w>DNA_ALPHABET</w>
-      <w>DNA_BASES</w>
-      <w>DNAbin2indel</w>
-      <w>DNAcopy</w>
-      <w>DNase</w>
-      <w>DO</w>
-      <w>DO.db</w>
-      <w>DO2ALLEG</w>
-      <w>DO2EG</w>
-      <w>DOANCESTOR</w>
-      <w>DOCHILDREN</w>
-      <w>DOIC</w>
-      <w>DOID</w>
-      <w>DOLite2EG</w>
-      <w>DOLiteTerm</w>
-      <w>DOMAPCOUNTS</w>
-      <w>DOOBSOLETE</w>
-      <w>DOOFFSPRING</w>
-      <w>DOPARENTS</w>
-      <w>DOSE</w>
-      <w>DOSYNONYM</w>
-      <w>DOTERM</w>
-      <w>DOTerms</w>
-      <w>DO_dbInfo</w>
-      <w>DO_dbconn</w>
-      <w>DO_dbfile</w>
-      <w>DO_dbschema</w>
-      <w>DRR</w>
-      <w>DSS</w>
-      <w>DSS.DE</w>
-      <w>DT</w>
-      <w>DTDATTR</w>
-      <w>DTDLOAD</w>
-      <w>DTDVALID</w>
-      <w>DTOutput</w>
-      <w>Dakar</w>
-      <w>Damascus</w>
-      <w>Danmarkshavn</w>
-      <w>Dar_es_Salaam</w>
-      <w>DarkTheme</w>
-      <w>Darwin</w>
-      <w>DatPkgFactory</w>
-      <w>DataFrame</w>
-      <w>DataFrameCallback</w>
-      <w>DataFrameList</w>
-      <w>DataToNChannelSet2</w>
-      <w>DataTrack</w>
-      <w>Davis</w>
-      <w>DavisThin</w>
-      <w>Dawson</w>
-      <w>Dawson_Creek</w>
-      <w>DefaultAssay</w>
-      <w>Definition</w>
-      <w>DelayedArray</w>
-      <w>Deltamatrix</w>
-      <w>DendSer.dendrogram</w>
-      <w>Denver</w>
-      <w>Depredations</w>
-      <w>DesignMatrix</w>
-      <w>DetailsAnnotationTrack</w>
-      <w>Detection</w>
-      <w>Detroit</w>
-      <w>Dhaka</w>
-      <w>Diagonal</w>
-      <w>Dialyzer</w>
-      <w>DietSeurat</w>
-      <w>Diff</w>
-      <w>DiffusionMaps</w>
-      <w>Digamma</w>
-      <w>Dili</w>
-      <w>Dim</w>
-      <w>DimHeatmap</w>
-      <w>DimPlot</w>
-      <w>DiscrFact</w>
-      <w>DiscreteRange</w>
-      <w>DisplayPars</w>
-      <w>Dist</w>
-      <w>Djibouti</w>
-      <w>DoEpiMod</w>
-      <w>DoExpMod</w>
-      <w>DoFEMbi</w>
-      <w>DoHeatmap</w>
-      <w>DoISVA</w>
-      <w>DoIntEpi450k</w>
-      <w>DoIntExp</w>
-      <w>DoIntFEM450k</w>
-      <w>Doctype</w>
-      <w>Dominica</w>
-      <w>DoparParam</w>
-      <w>DotPlot</w>
-      <w>Dotplot</w>
-      <w>Douala</w>
-      <w>DrL</w>
-      <w>Dubai</w>
-      <w>Dublin</w>
-      <w>DumontDUrville</w>
-      <w>Duncan</w>
-      <w>Duplicated</w>
-      <w>Dups</w>
-      <w>Dushanbe</w>
-      <w>Dwyer</w>
-      <w>E</w>
-      <w>EBMTP</w>
-      <w>EBupdate</w>
-      <w>EEF.profile</w>
-      <w>EET</w>
-      <w>EG2ALLDO</w>
-      <w>EG2DO</w>
-      <w>EG2DOLite</w>
-      <w>EIC</w>
-      <w>EL.profile</w>
-      <w>ELISA</w>
-      <w>EMPTY</w>
-      <w>ENSEMBLIdentifier</w>
-      <w>EPICSimData</w>
-      <w>EST</w>
-      <w>EWCE</w>
-      <w>EXTID2NAME</w>
-      <w>E_loo</w>
-      <w>Earthquake</w>
-      <w>EastAuClimate</w>
-      <w>Easter</w>
-      <w>EasterMonday</w>
-      <w>EasterSunday</w>
-      <w>Eastern</w>
-      <w>Ecdf</w>
-      <w>Edmonton</w>
-      <w>Efate</w>
-      <w>Eirunepe</w>
-      <w>El_Aaiun</w>
-      <w>El_Salvador</w>
-      <w>ElbowPlot</w>
-      <w>Embeddings</w>
-      <w>Encoding</w>
-      <w>EndRule</w>
-      <w>Enderbury</w>
-      <w>EnsDb</w>
-      <w>EntrezFilter</w>
-      <w>EntrezIdentifier</w>
-      <w>EntrezidFilter</w>
-      <w>EnzymeIdentifier</w>
-      <w>Epiphany</w>
-      <w>Ericksen</w>
-      <w>EstDimIC</w>
-      <w>EstDimRMT</w>
-      <w>EuStockMarkets</w>
-      <w>Eucla</w>
-      <w>EventHistory.frame</w>
-      <w>ExLinear</w>
-      <w>ExNPreg</w>
-      <w>ExNclus</w>
-      <w>Exception</w>
-      <w>ExonEndFilter</w>
-      <w>ExonIdFilter</w>
-      <w>ExonNameFilter</w>
-      <w>ExonRankFilter</w>
-      <w>ExonStartFilter</w>
-      <w>ExonidFilter</w>
-      <w>ExonrankFilter</w>
-      <w>Exp.cov</w>
-      <w>Exp.earth.cov</w>
-      <w>Exp.image.cov</w>
-      <w>Exp.simple.cov</w>
-      <w>ExpMean</w>
-      <w>ExpSD</w>
-      <w>ExpVar</w>
-      <w>Expand</w>
-      <w>ExperimentList</w>
-      <w>ExperimentPath</w>
-      <w>Exponential</w>
-      <w>ExponentialUpper</w>
-      <w>ExponentialUpperC</w>
-      <w>Export</w>
-      <w>ExportToCellbrowser</w>
-      <w>ExposeAttribute</w>
-      <w>ExpressionSet</w>
-      <w>ExpressionSetCollection</w>
-      <w>F</w>
-      <w>FAMD</w>
-      <w>FANTOM5humanSamples</w>
-      <w>FANTOM5mouseSamples</w>
-      <w>FAQ</w>
-      <w>FDb.InfiniumMethylation.hg19</w>
-      <w>FEM</w>
-      <w>FFdes</w>
-      <w>FG</w>
-      <w>FKS</w>
-      <w>FLAG_BITNAMES</w>
-      <w>FLXMCdist1</w>
-      <w>FLXMCfactanal</w>
-      <w>FLXMCmvbinary</w>
-      <w>FLXMCmvcombi</w>
-      <w>FLXMCmvnorm</w>
-      <w>FLXMCmvpois</w>
-      <w>FLXMCnorm1</w>
-      <w>FLXMRcondlogit</w>
-      <w>FLXMRglm</w>
-      <w>FLXMRglmfix</w>
-      <w>FLXMRglmnet</w>
-      <w>FLXMRlmer</w>
-      <w>FLXMRlmm</w>
-      <w>FLXMRlmmc</w>
-      <w>FLXMRmgcv</w>
-      <w>FLXMRmultinom</w>
-      <w>FLXMRrobglm</w>
-      <w>FLXMRziglm</w>
-      <w>FLXPconstant</w>
-      <w>FLXPmultinom</w>
-      <w>FLXbclust</w>
-      <w>FLXcheckComponent</w>
-      <w>FLXconstant</w>
-      <w>FLXdeterminePostunscaled</w>
-      <w>FLXdist</w>
-      <w>FLXfit</w>
-      <w>FLXgetDesign</w>
-      <w>FLXgetK</w>
-      <w>FLXgetModelmatrix</w>
-      <w>FLXgetObs</w>
-      <w>FLXgetParameters</w>
-      <w>FLXglm</w>
-      <w>FLXglmFix</w>
-      <w>FLXgradlogLikfun</w>
-      <w>FLXlogLikfun</w>
-      <w>FLXmclust</w>
-      <w>FLXmstep</w>
-      <w>FLXmultinom</w>
-      <w>FLXremoveComponent</w>
-      <w>FLXreplaceParameters</w>
-      <w>FM_index</w>
-      <w>FM_index_R</w>
-      <w>FM_index_permutation</w>
-      <w>FM_index_profdpm</w>
-      <w>FNN</w>
-      <w>FOBI</w>
-      <w>FRAllSaints</w>
-      <w>FRArmisticeDay</w>
-      <w>FRAscension</w>
-      <w>FRAssumptionVirginMary</w>
-      <w>FRBastilleDay</w>
-      <w>FRFetDeLaVictoire1945</w>
-      <w>FStat</w>
-      <w>FX</w>
-      <w>F_meas</w>
-      <w>FaFile</w>
-      <w>FaFileList</w>
-      <w>Facet</w>
-      <w>FacetGrid</w>
-      <w>FacetNull</w>
-      <w>FacetWrap</w>
-      <w>FactoMineR</w>
-      <w>FactorList</w>
-      <w>Fakaofo</w>
-      <w>Faroe</w>
-      <w>FastICA</w>
-      <w>FastaFile</w>
-      <w>FastqFile</w>
-      <w>FastqFileList</w>
-      <w>FastqQuality</w>
-      <w>FastqSampler</w>
-      <w>FastqSamplerList</w>
-      <w>FastqStreamer</w>
-      <w>FastqStreamerList</w>
-      <w>Fatigue</w>
-      <w>FeatureLocator</w>
-      <w>FeaturePlot</w>
-      <w>FeatureScatter</w>
-      <w>FemModShow</w>
-      <w>FetchData</w>
-      <w>Fiji</w>
-      <w>FileDep</w>
-      <w>FileForFormat</w>
-      <w>FileProgressBar</w>
-      <w>Filter</w>
-      <w>FilterMatrix</w>
-      <w>FilterRules</w>
-      <w>Find</w>
-      <w>FindAllMarkers</w>
-      <w>FindClusters</w>
-      <w>FindConservedMarkers</w>
-      <w>FindIntegrationAnchors</w>
-      <w>FindMarkers</w>
-      <w>FindNeighbors</w>
-      <w>FindTransferAnchors</w>
-      <w>FindVariableFeatures</w>
-      <w>FiveUTRVariants</w>
-      <w>Florida</w>
-      <w>FlowSorted.DLPFC.450k</w>
-      <w>FontSize</w>
-      <w>Formaldehyde</w>
-      <w>Formula</w>
-      <w>Fortaleza</w>
-      <w>Frankenstein</w>
-      <w>Frankfurt</w>
-      <w>Freedman</w>
-      <w>Freetown</w>
-      <w>Friendly</w>
-      <w>FruchtermanReingold</w>
-      <w>Ftab</w>
-      <w>Funafuti</w>
-      <w>Function</w>
-      <w>Future</w>
-      <w>FutureCondition</w>
-      <w>FutureError</w>
-      <w>FutureGlobals</w>
-      <w>FutureMessage</w>
-      <w>FutureResult</w>
-      <w>FutureWarning</w>
-      <w>G.VS</w>
-      <w>GAGurine</w>
-      <w>GAlignmentPairs</w>
-      <w>GAlignments</w>
-      <w>GAlignmentsList</w>
-      <w>GBBankHoliday</w>
-      <w>GBMayDay</w>
-      <w>GBMilleniumDay</w>
-      <w>GBSummerBankHoliday</w>
-      <w>GC.content</w>
-      <w>GCD</w>
-      <w>GCcontent</w>
-      <w>GDS2MA</w>
-      <w>GDS2eSet</w>
-      <w>GENETIC_CODE</w>
-      <w>GENETIC_CODE_TABLE</w>
-      <w>GEOquery</w>
-      <w>GET</w>
-      <w>GE_SpatialGrid</w>
-      <w>GFF1File</w>
-      <w>GFF2File</w>
-      <w>GFF3File</w>
-      <w>GFFFile</w>
-      <w>GFFcolnames</w>
-      <w>GGally</w>
-      <w>GLtoGP</w>
-      <w>GM2.lvm</w>
-      <w>GM3.lvm</w>
-      <w>GNCList</w>
-      <w>GO</w>
-      <w>GO.db</w>
-      <w>GO2AllProbes</w>
-      <w>GO2heatmap</w>
-      <w>GOAllFrame</w>
-      <w>GOAllFrameIdentifier</w>
-      <w>GOBPANCESTOR</w>
-      <w>GOBPCHILDREN</w>
-      <w>GOBPOFFSPRING</w>
-      <w>GOBPPARENTS</w>
-      <w>GOCCANCESTOR</w>
-      <w>GOCCCHILDREN</w>
-      <w>GOCCOFFSPRING</w>
-      <w>GOCCPARENTS</w>
-      <w>GOCluster_Report</w>
-      <w>GOCollection</w>
-      <w>GOFisherTest</w>
-      <w>GOFrame</w>
-      <w>GOGraph</w>
-      <w>GOHyperGAll</w>
-      <w>GOHyperGAll_Simplify</w>
-      <w>GOHyperGAll_Subset</w>
-      <w>GOID</w>
-      <w>GOKSTest</w>
-      <w>GOKSTiesTest</w>
-      <w>GOMAPCOUNTS</w>
-      <w>GOMFANCESTOR</w>
-      <w>GOMFCHILDREN</w>
-      <w>GOMFOFFSPRING</w>
-      <w>GOMFPARENTS</w>
-      <w>GOOBSOLETE</w>
-      <w>GOSYNONYM</w>
-      <w>GOSemSim</w>
-      <w>GOSumTest</w>
-      <w>GOTERM</w>
-      <w>GOTerms</w>
-      <w>GO_dbInfo</w>
-      <w>GO_dbconn</w>
-      <w>GO_dbfile</w>
-      <w>GO_dbschema</w>
-      <w>GOdata</w>
-      <w>GOglobalTest</w>
-      <w>GOmnplot</w>
-      <w>GOplot</w>
-      <w>GOstats</w>
-      <w>GOtTest</w>
-      <w>GPA</w>
-      <w>GPL</w>
-      <w>GPLList</w>
-      <w>GPos</w>
-      <w>GRangePairs</w>
-      <w>GRanges</w>
-      <w>GRangesFilter</w>
-      <w>GRangesForBSGenome</w>
-      <w>GRangesForUCSCGenome</w>
-      <w>GRangesList</w>
-      <w>GRoperator</w>
-      <w>GSEABase</w>
-      <w>GSEAGOHyperGParams</w>
-      <w>GSEAKEGGHyperGParams</w>
-      <w>GSMList</w>
-      <w>GSSvocab</w>
-      <w>GSVA</w>
-      <w>GString</w>
-      <w>GTFFile</w>
-      <w>GVFFile</w>
-      <w>GVME</w>
-      <w>GVME_Consensus</w>
-      <w>Gaborone</w>
-      <w>Galapagos</w>
-      <w>Gambier</w>
-      <w>Gamma</w>
-      <w>Gamma.lvm</w>
-      <w>GappedReads</w>
-      <w>Gasoline</w>
-      <w>Gaza</w>
-      <w>Geary</w>
-      <w>GearyLocal</w>
-      <w>GenStatM</w>
-      <w>GenStatMsp</w>
-      <w>GenStatR</w>
-      <w>GenTable</w>
-      <w>GeneBiotypeFilter</w>
-      <w>GeneColorSet</w>
-      <w>GeneEndFilter</w>
-      <w>GeneIdFilter</w>
-      <w>GeneRegionTrack</w>
-      <w>GeneSet</w>
-      <w>GeneSetCollection</w>
-      <w>GeneStartFilter</w>
-      <w>GenebiotypeFilter</w>
-      <w>GeneidFilter</w>
-      <w>GenenameFilter</w>
-      <w>GenenameIdentifier</w>
-      <w>GenericSummary</w>
-      <w>GenomeAxisTrack</w>
-      <w>GenomeDescription</w>
-      <w>GenomeInfoDb</w>
-      <w>GenomeInfoDbData</w>
-      <w>GenomicAlignments</w>
-      <w>GenomicData</w>
-      <w>GenomicFeatures</w>
-      <w>GenomicMethylSet</w>
-      <w>GenomicRanges</w>
-      <w>GenomicRangesList</w>
-      <w>GenomicRatioSet</w>
-      <w>GenomicSelection</w>
-      <w>GenzBretz</w>
-      <w>Geom</w>
-      <w>GeomAbline</w>
-      <w>GeomAnnotationMap</w>
-      <w>GeomArea</w>
-      <w>GeomBar</w>
-      <w>GeomBlank</w>
-      <w>GeomBoxplot</w>
-      <w>GeomCol</w>
-      <w>GeomContour</w>
-      <w>GeomCrossbar</w>
-      <w>GeomCurve</w>
-      <w>GeomCustomAnn</w>
-      <w>GeomDensity</w>
-      <w>GeomDensity2d</w>
-      <w>GeomDensityLine</w>
-      <w>GeomDensityRidges</w>
-      <w>GeomDensityRidges2</w>
-      <w>GeomDensityRidgesGradient</w>
-      <w>GeomDotplot</w>
-      <w>GeomDrawGrob</w>
-      <w>GeomErrorbar</w>
-      <w>GeomErrorbarh</w>
-      <w>GeomHex</w>
-      <w>GeomHline</w>
-      <w>GeomLabel</w>
-      <w>GeomLabelRepel</w>
-      <w>GeomLine</w>
-      <w>GeomLinerange</w>
-      <w>GeomLogticks</w>
-      <w>GeomMap</w>
-      <w>GeomPath</w>
-      <w>GeomPoint</w>
-      <w>GeomPointrange</w>
-      <w>GeomPolygon</w>
-      <w>GeomQuantile</w>
-      <w>GeomRaster</w>
-      <w>GeomRasterAnn</w>
-      <w>GeomRect</w>
-      <w>GeomRibbon</w>
-      <w>GeomRidgeline</w>
-      <w>GeomRidgelineGradient</w>
-      <w>GeomRug</w>
-      <w>GeomSegment</w>
-      <w>GeomSf</w>
-      <w>GeomSmooth</w>
-      <w>GeomSpoke</w>
-      <w>GeomStep</w>
-      <w>GeomText</w>
-      <w>GeomTextRepel</w>
-      <w>GeomTile</w>
-      <w>GeomVRidgeline</w>
-      <w>GeomViolin</w>
-      <w>GeomVline</w>
-      <w>GermanCredit</w>
-      <w>GetAssay</w>
-      <w>GetAssayData</w>
-      <w>GetColor</w>
-      <w>GetIntegrationData</w>
-      <w>GetModelFrame</w>
-      <w>Gibraltar</w>
-      <w>GiniMd</w>
-      <w>Ginzberg</w>
-      <w>Glace_Bay</w>
-      <w>GlaucomaMVF</w>
-      <w>Gleser</w>
-      <w>Globals</w>
-      <w>Glucose</w>
-      <w>Glucose2</w>
-      <w>Godthab</w>
-      <w>Gompertz2</w>
-      <w>GoodFriday</w>
-      <w>Goose_Bay</w>
-      <w>Gorsuch</w>
-      <w>Grand_Turk</w>
-      <w>Graph</w>
-      <w>Greene</w>
-      <w>Grenada</w>
-      <w>Grep</w>
-      <w>GridTopology</w>
-      <w>Guadalcanal</w>
-      <w>Guadeloupe</w>
-      <w>Guam</w>
-      <w>Guatemala</w>
-      <w>Guayaquil</w>
-      <w>Guernsey</w>
-      <w>Gun</w>
-      <w>Guyana</w>
-      <w>Guyer</w>
-      <w>Gviz</w>
-      <w>H0</w>
-      <w>H2LGrouping</w>
-      <w>H5Aclose</w>
-      <w>H5Acreate</w>
-      <w>H5Adelete</w>
-      <w>H5Aexists</w>
-      <w>H5Aget_name</w>
-      <w>H5Aget_space</w>
-      <w>H5Aget_type</w>
-      <w>H5Aopen</w>
-      <w>H5Aopen_by_idx</w>
-      <w>H5Aopen_by_name</w>
-      <w>H5Aread</w>
-      <w>H5Awrite</w>
-      <w>H5Dclose</w>
-      <w>H5Dcreate</w>
-      <w>H5Dget_create_plist</w>
-      <w>H5Dget_space</w>
-      <w>H5Dget_storage_size</w>
-      <w>H5Dget_type</w>
-      <w>H5Dopen</w>
-      <w>H5Dread</w>
-      <w>H5Dset_extent</w>
-      <w>H5Dwrite</w>
-      <w>H5Fclose</w>
-      <w>H5Fcreate</w>
-      <w>H5Fflush</w>
-      <w>H5Fget_access_plist</w>
-      <w>H5Fget_create_plist</w>
-      <w>H5Fget_filesize</w>
-      <w>H5Fget_name</w>
-      <w>H5Fis_hdf5</w>
-      <w>H5Fopen</w>
-      <w>H5Gclose</w>
-      <w>H5Gcreate</w>
-      <w>H5Gcreate_anon</w>
-      <w>H5Gget_info</w>
-      <w>H5Gget_info_by_idx</w>
-      <w>H5Gget_info_by_name</w>
-      <w>H5Gopen</w>
-      <w>H5Iget_name</w>
-      <w>H5Iget_type</w>
-      <w>H5Iis_valid</w>
-      <w>H5Lcreate_external</w>
-      <w>H5Lexists</w>
-      <w>H5Lget_info</w>
-      <w>H5Oclose</w>
-      <w>H5Oget_num_attrs</w>
-      <w>H5Oget_num_attrs_by_name</w>
-      <w>H5Oopen</w>
-      <w>H5Pclose</w>
-      <w>H5Pclose_class</w>
-      <w>H5Pcopy</w>
-      <w>H5Pcreate</w>
-      <w>H5Pequal</w>
-      <w>H5Pfill_value_defined</w>
-      <w>H5Pget_alloc_time</w>
-      <w>H5Pget_char_encoding</w>
-      <w>H5Pget_chunk</w>
-      <w>H5Pget_class</w>
-      <w>H5Pget_create_intermediate_group</w>
-      <w>H5Pget_fill_time</w>
-      <w>H5Pget_layout</w>
-      <w>H5Pget_libver_bounds</w>
-      <w>H5Pset_alloc_time</w>
-      <w>H5Pset_char_encoding</w>
-      <w>H5Pset_chunk</w>
-      <w>H5Pset_chunk_cache</w>
-      <w>H5Pset_create_intermediate_group</w>
-      <w>H5Pset_deflate</w>
-      <w>H5Pset_fill_time</w>
-      <w>H5Pset_fill_value</w>
-      <w>H5Pset_layout</w>
-      <w>H5Pset_libver_bounds</w>
-      <w>H5Sclose</w>
-      <w>H5Scopy</w>
-      <w>H5Screate</w>
-      <w>H5Screate_simple</w>
-      <w>H5Sget_simple_extent_dims</w>
-      <w>H5Sis_simple</w>
-      <w>H5Sselect_hyperslab</w>
-      <w>H5Sselect_index</w>
-      <w>H5Sset_extent_simple</w>
-      <w>H5Tcopy</w>
-      <w>H5Tset_size</w>
-      <w>H5close</w>
-      <w>H5garbage_collect</w>
-      <w>H5get_libversion</w>
-      <w>H5open</w>
-      <w>HCPC</w>
-      <w>HDF5Array</w>
-      <w>HDF5ArraySeed</w>
-      <w>HDF5RealizationSink</w>
-      <w>HDPHMMnegbin</w>
-      <w>HDPHMMpoisson</w>
-      <w>HDPHSMMnegbin</w>
-      <w>HEAD</w>
-      <w>HGID2homology</w>
-      <w>HGNChelper</w>
-      <w>HLLE</w>
-      <w>HLS</w>
-      <w>HMFA</w>
-      <w>HMMpanelFE</w>
-      <w>HMMpanelRE</w>
-      <w>HNF4alpha</w>
-      <w>HP.links</w>
-      <w>HPDinterval</w>
-      <w>HSV</w>
-      <w>HTML</w>
-      <w>HTMLheader</w>
-      <w>HTODemux</w>
-      <w>HTOHeatmap</w>
-      <w>HTTP_VERSION_1_0</w>
-      <w>HTTP_VERSION_1_1</w>
-      <w>HTTP_VERSION_LAST</w>
-      <w>HTTP_VERSION_NONE</w>
-      <w>HUGE</w>
-      <w>HULK</w>
-      <w>HVFInfo</w>
-      <w>Habituationdata</w>
-      <w>HairEyeColor</w>
-      <w>Halifax</w>
-      <w>Harare</w>
-      <w>Harbin</w>
-      <w>Harman.5</w>
-      <w>Harman.8</w>
-      <w>Harman.political</w>
-      <w>Harman23.cor</w>
-      <w>Harman74.cor</w>
-      <w>Hartnagel</w>
-      <w>Havana</w>
-      <w>Helsinki</w>
-      <w>Hermosillo</w>
-      <w>Hershey</w>
-      <w>HexPoints2SpatialPolygons</w>
-      <w>HighlightTrack</w>
-      <w>Highway1</w>
-      <w>Hilbert</w>
-      <w>Hist</w>
-      <w>Hits</w>
-      <w>HitsList</w>
-      <w>Hmisc</w>
-      <w>Hobart</w>
-      <w>HoltWinters</w>
-      <w>Holzinger</w>
-      <w>Holzinger.9</w>
-      <w>HongKong</w>
-      <w>Hong_Kong</w>
-      <w>Honolulu</w>
-      <w>Hovd</w>
-      <w>HoverLocator</w>
-      <w>Hsapiens</w>
-      <w>Hsets</w>
-      <w>HttpClient</w>
-      <w>HttpRequest</w>
-      <w>HttpResponse</w>
-      <w>I</w>
-      <w>IC.Cor.NA</w>
-      <w>IC.CorXW.NA</w>
-      <w>ICC</w>
-      <w>ICC2latex</w>
-      <w>ICL</w>
-      <w>ICLUST</w>
-      <w>ICLUST.cluster</w>
-      <w>ICLUST.graph</w>
-      <w>ICLUST.rgraph</w>
-      <w>ICLUST.sort</w>
-      <w>ID2EntrezID</w>
-      <w>ID2GO</w>
-      <w>ID2KEGG</w>
-      <w>IDATsToMatrices</w>
-      <w>IDATsToMatrices2</w>
-      <w>IDATtoMatrix</w>
-      <w>IDATtoMatrix2</w>
-      <w>IDateTime</w>
-      <w>IDvaluesGridTopology</w>
-      <w>IDvaluesSpatialPixels</w>
-      <w>IGF</w>
-      <w>IHW</w>
-      <w>IMCAEntrezLink</w>
-      <w>IPos</w>
-      <w>IQR</w>
-      <w>IRanges</w>
-      <w>IRangesList</w>
-      <w>ISOdate</w>
-      <w>ISOdatetime</w>
-      <w>ITAllSaints</w>
-      <w>ITAssumptionOfVirginMary</w>
-      <w>ITEpiphany</w>
-      <w>ITImmaculateConception</w>
-      <w>ITLiberationDay</w>
-      <w>ITStAmrose</w>
-      <w>IUPAC_CODE_MAP</w>
-      <w>IV</w>
-      <w>Id</w>
-      <w>Identical</w>
-      <w>Identify3d</w>
-      <w>Idents</w>
-      <w>IdeogramTrack</w>
-      <w>Illumina450ProbeVariants.db</w>
-      <w>IlluminaHumanMethylation450kanno.ilmn12.hg19</w>
-      <w>IlluminaHumanMethylation450kmanifest</w>
-      <w>IlluminaHumanMethylationEPICanno.ilm10b2.hg19</w>
-      <w>IlluminaHumanMethylationEPICmanifest</w>
-      <w>IlluminaID2nuID</w>
-      <w>IlluminaMethylationAnnotation</w>
-      <w>IlluminaMethylationManifest</w>
-      <w>IlluminaQuality</w>
-      <w>Im</w>
-      <w>ImageDiff</w>
-      <w>Import</w>
-      <w>ImputeByMean</w>
-      <w>Indianapolis</w>
-      <w>Indometh</w>
-      <w>Initialize</w>
-      <w>InsectSprays</w>
-      <w>Insurance</w>
-      <w>IntegerList</w>
-      <w>IntegerQuality</w>
-      <w>IntegrateData</w>
-      <w>Interface</w>
-      <w>IntergenicVariants</w>
-      <w>InternalErrorException</w>
-      <w>IntersectionNotEmpty</w>
-      <w>IntersectionStrict</w>
-      <w>Intervals</w>
-      <w>Intervals_full</w>
-      <w>IntronVariants</w>
-      <w>Inuvik</w>
-      <w>Inverse</w>
-      <w>Iqaluit</w>
-      <w>Irkutsk</w>
-      <w>Islands.UCSC</w>
-      <w>Isle_of_Man</w>
-      <w>Isomap</w>
-      <w>Istanbul</w>
-      <w>Istat</w>
-      <w>JADE</w>
-      <w>JDEoptim</w>
-      <w>JO</w>
-      <w>JPAutumnalEquinox</w>
-      <w>JPBankHolidayDec31</w>
-      <w>JPBankHolidayJan2</w>
-      <w>JPBankHolidayJan3</w>
-      <w>JPBunkaNoHi</w>
-      <w>JPChildrensDay</w>
-      <w>JPComingOfAgeDay</w>
-      <w>JPConstitutionDay</w>
-      <w>JPEmperorsBirthday</w>
-      <w>JPGantan</w>
-      <w>JPGreeneryDay</w>
-      <w>JPHealthandSportsDay</w>
-      <w>JPKeirouNOhi</w>
-      <w>JPKenkokuKinenNoHi</w>
-      <w>JPKenpouKinenBi</w>
-      <w>JPKinrouKanshaNoHi</w>
-      <w>JPKodomoNoHi</w>
-      <w>JPKokuminNoKyujitu</w>
-      <w>JPMarineDay</w>
-      <w>JPMidoriNoHi</w>
-      <w>JPNatFoundationDay</w>
-      <w>JPNationHoliday</w>
-      <w>JPNationalCultureDay</w>
-      <w>JPNewYearsDay</w>
-      <w>JPRespectForTheAgedDay</w>
-      <w>JPSeijinNoHi</w>
-      <w>JPShuubunNoHi</w>
-      <w>JPTaiikuNoHi</w>
-      <w>JPTennouTanjyouBi</w>
-      <w>JPThanksgivingDay</w>
-      <w>JPUmiNoHi</w>
-      <w>JPVernalEquinox</w>
-      <w>JS</w>
-      <w>JackStraw</w>
-      <w>JackStrawPlot</w>
-      <w>Jakarta</w>
-      <w>Jamaica</w>
-      <w>Java</w>
-      <w>Jayapura</w>
-      <w>Jersey</w>
-      <w>Jerusalem</w>
-      <w>Johannesburg</w>
-      <w>JohnsonJohnson</w>
-      <w>Johnston</w>
-      <w>Jujuy</w>
-      <w>Juneau</w>
-      <w>KALLISTO_ASSAYS</w>
-      <w>KEGG2AllProbes</w>
-      <w>KEGG2heatmap</w>
-      <w>KEGGCollection</w>
-      <w>KEGGFrame</w>
-      <w>KEGGREST</w>
-      <w>KEGGmnplot</w>
-      <w>KL.dist</w>
-      <w>KL.divergence</w>
-      <w>KLdiv</w>
-      <w>KLx.dist</w>
-      <w>KLx.divergence</w>
-      <w>KML</w>
-      <w>KMO</w>
-      <w>KNex</w>
-      <w>KRmodcomp</w>
-      <w>KRmodcomp.lmerMod</w>
-      <w>KRmodcomp.mer</w>
-      <w>KRmodcomp_init</w>
-      <w>KRmodcomp_init.lmerMod</w>
-      <w>KRmodcomp_init.mer</w>
-      <w>KRmodcomp_internal</w>
-      <w>KSd</w>
-      <w>Kabul</w>
-      <w>Kaliningrad</w>
-      <w>KalmanForecast</w>
-      <w>KalmanLike</w>
-      <w>KalmanRun</w>
-      <w>KalmanSmooth</w>
-      <w>KamadaKawai</w>
-      <w>Kamchatka</w>
-      <w>Kampala</w>
-      <w>Kappa</w>
-      <w>Karachi</w>
-      <w>Kashgar</w>
-      <w>Katmandu</w>
-      <w>Kaver</w>
-      <w>Kenvl</w>
-      <w>Kerguelen</w>
-      <w>KernSmooth</w>
-      <w>KernelSums</w>
-      <w>KernelTest</w>
-      <w>Key</w>
-      <w>Key2</w>
-      <w>Kfn</w>
-      <w>Khartoum</w>
-      <w>KhatriRao</w>
-      <w>KhmaladzeTest</w>
-      <w>Kiev</w>
-      <w>Kigali</w>
-      <w>Kinshasa</w>
-      <w>Kinship82</w>
-      <w>Kinship82_Consensus</w>
-      <w>Kiritimati</w>
-      <w>Kline</w>
-      <w>Knox</w>
-      <w>Kosrae</w>
-      <w>KosteckiDillon</w>
-      <w>Krasnoyarsk</w>
-      <w>Krig</w>
-      <w>Krig.Amatrix</w>
-      <w>Krig.check.xY</w>
-      <w>Krig.coef</w>
-      <w>Krig.cor.Y</w>
-      <w>Krig.df.to.lambda</w>
-      <w>Krig.engine.default</w>
-      <w>Krig.engine.fixed</w>
-      <w>Krig.engine.knots</w>
-      <w>Krig.fdf</w>
-      <w>Krig.fgcv</w>
-      <w>Krig.fgcv.model</w>
-      <w>Krig.fgcv.one</w>
-      <w>Krig.flplike</w>
-      <w>Krig.fs2hat</w>
-      <w>Krig.ftrace</w>
-      <w>Krig.make.W</w>
-      <w>Krig.make.Wi</w>
-      <w>Krig.make.u</w>
-      <w>Krig.null.function</w>
-      <w>Krig.parameters</w>
-      <w>Krig.replicates</w>
-      <w>Krig.transform.xY</w>
-      <w>Krig.updateY</w>
-      <w>Krig.which.lambda</w>
-      <w>Krig.ynew</w>
-      <w>KualaLumpur</w>
-      <w>Kuala_Lumpur</w>
-      <w>Kuching</w>
-      <w>Kuwait</w>
-      <w>Kwajalein</w>
-      <w>L2CCA</w>
-      <w>L2Dim</w>
-      <w>L2metric</w>
-      <w>LAB</w>
-      <w>LCM</w>
-      <w>LCMC</w>
-      <w>LComments</w>
-      <w>LDEsysMat</w>
-      <w>LDSearch</w>
-      <w>LETTERS</w>
-      <w>LL2homology</w>
-      <w>LLE</w>
-      <w>LLint</w>
-      <w>LMM_Sigma_G</w>
-      <w>LPH07_1</w>
-      <w>LPH07_2</w>
-      <w>LR_test</w>
-      <w>LTT</w>
-      <w>LUV</w>
-      <w>La.svd</w>
-      <w>La_Paz</w>
-      <w>La_Rioja</w>
-      <w>La_library</w>
-      <w>La_version</w>
-      <w>Label</w>
-      <w>LabelClusters</w>
-      <w>LabelPoints</w>
-      <w>LaborDay</w>
-      <w>Lag</w>
-      <w>Lagos</w>
-      <w>LakeHuron</w>
-      <w>LaplacianEigenmaps</w>
-      <w>Lapply</w>
-      <w>Layout</w>
-      <w>Lb_ddf</w>
-      <w>LdFlags</w>
-      <w>LdaClassic</w>
-      <w>LdaPP</w>
-      <w>Leinhardt</w>
-      <w>Lencoding</w>
-      <w>LiblineaR</w>
-      <w>Libreville</w>
-      <w>LifeCycleSavings</w>
-      <w>Lima</w>
-      <w>LinGray</w>
-      <w>LinOCS</w>
-      <w>Linda</w>
-      <w>Lindeman</w>
-      <w>Line</w>
-      <w>LineLength</w>
-      <w>Lines</w>
-      <w>LinesLength</w>
-      <w>Lisbon</w>
-      <w>List</w>
-      <w>List2Matrix</w>
-      <w>ListCallback</w>
-      <w>Ljubljana</w>
-      <w>Lkeyname</w>
-      <w>Lkeys</w>
-      <w>Llength</w>
-      <w>Lnjunc</w>
-      <w>LoBD</w>
-      <w>Load</w>
-      <w>Loadings</w>
-      <w>Loblolly</w>
-      <w>LocalStruct</w>
-      <w>Locations</w>
-      <w>Loffset</w>
-      <w>LogFC</w>
-      <w>LogNormalize</w>
-      <w>LogOdds</w>
-      <w>LogSeuratCommand</w>
-      <w>LogVMR</w>
-      <w>Logic</w>
-      <w>LogicalList</w>
-      <w>LogitBoost</w>
-      <w>Lognorm2</w>
-      <w>Lome</w>
-      <w>London</w>
-      <w>Longyearbyen</w>
-      <w>Lord_Howe</w>
-      <w>LosAngeles</w>
-      <w>Los_Angeles</w>
-      <w>Louisville</w>
-      <w>Luanda</w>
-      <w>Lubumbashi</w>
-      <w>Lusaka</w>
-      <w>Luxembourg</w>
-      <w>M2Beta</w>
-      <w>M5data</w>
-      <w>MA.RG</w>
-      <w>MAE</w>
-      <w>MAGMA.Celltyping</w>
-      <w>MAPAmat</w>
-      <w>MAPKsig</w>
-      <w>MASS</w>
-      <w>MATCH</w>
-      <w>MATCH.default</w>
-      <w>MATCH.times</w>
-      <w>MAplot</w>
-      <w>MCA</w>
-      <w>MCMCSVDreg</w>
-      <w>MCMCbinaryChange</w>
-      <w>MCMCdynamicEI</w>
-      <w>MCMCdynamicIRT1d</w>
-      <w>MCMCfactanal</w>
-      <w>MCMChierEI</w>
-      <w>MCMChlogit</w>
-      <w>MCMChpoisson</w>
-      <w>MCMChregress</w>
-      <w>MCMCirt1d</w>
-      <w>MCMCirtHier1d</w>
-      <w>MCMCirtKd</w>
-      <w>MCMCirtKdRob</w>
-      <w>MCMClogit</w>
-      <w>MCMCmetrop1R</w>
-      <w>MCMCmixfactanal</w>
-      <w>MCMCmnl</w>
-      <w>MCMCnegbin</w>
-      <w>MCMCnegbinChange</w>
-      <w>MCMCoprobit</w>
-      <w>MCMCoprobitChange</w>
-      <w>MCMCordfactanal</w>
-      <w>MCMCpack</w>
-      <w>MCMCpoisson</w>
-      <w>MCMCpoissonChange</w>
-      <w>MCMCprobit</w>
-      <w>MCMCprobitChange</w>
-      <w>MCMCquantreg</w>
-      <w>MCMCregress</w>
-      <w>MCMCregressChange</w>
-      <w>MCMCresidualBreakAnalysis</w>
-      <w>MCMCtobit</w>
-      <w>MCbinomialbeta</w>
-      <w>MCmultinomdirichlet</w>
-      <w>MCnormalnormal</w>
-      <w>MCpoissongamma</w>
-      <w>MD</w>
-      <w>MDS</w>
-      <w>MEapply</w>
-      <w>MFA</w>
-      <w>MIAME</w>
-      <w>MISSING</w>
-      <w>MLE.Matern</w>
-      <w>MLE.Matern.fast</w>
-      <w>MLE.objective.fn</w>
-      <w>MLESpatialProcess</w>
-      <w>MLESpatialProcess.fast</w>
-      <w>MOFAtools</w>
-      <w>MPR</w>
-      <w>MPpenalty</w>
-      <w>MSEP</w>
-      <w>MST</w>
-      <w>MSbetween</w>
-      <w>MSwithin</w>
-      <w>MTP</w>
-      <w>MULTIseqDemux</w>
-      <w>MW.nm1</w>
-      <w>MW.nm10</w>
-      <w>MW.nm11</w>
-      <w>MW.nm12</w>
-      <w>MW.nm13</w>
-      <w>MW.nm14</w>
-      <w>MW.nm15</w>
-      <w>MW.nm16</w>
-      <w>MW.nm2</w>
-      <w>MW.nm2.old</w>
-      <w>MW.nm3</w>
-      <w>MW.nm4</w>
-      <w>MW.nm5</w>
-      <w>MW.nm6</w>
-      <w>MW.nm7</w>
-      <w>MW.nm8</w>
-      <w>MW.nm9</w>
-      <w>Macau</w>
-      <w>Maceio</w>
-      <w>Machines</w>
-      <w>Madeira</w>
-      <w>Madrid</w>
-      <w>Magadan</w>
-      <w>Mahe</w>
-      <w>Majuro</w>
-      <w>Makassar</w>
-      <w>Makesense</w>
-      <w>Malabo</w>
-      <w>Maldives</w>
-      <w>Malta</w>
-      <w>Mammals</w>
-      <w>Managua</w>
-      <w>Manaus</w>
-      <w>Mandel</w>
-      <w>Mandible</w>
-      <w>Manifest</w>
-      <w>Manila</w>
-      <w>Manova</w>
-      <w>ManyToManyGrouping</w>
-      <w>ManyToOneGrouping</w>
-      <w>Map</w>
-      <w>MapCollection</w>
-      <w>MapGen2SL</w>
-      <w>Maputo</w>
-      <w>Marengo</w>
-      <w>Mariehamn</w>
-      <w>Marigot</w>
-      <w>Marquesas</w>
-      <w>Martinique</w>
-      <w>Maseru</w>
-      <w>Mask</w>
-      <w>MaskCollection.show_frame</w>
-      <w>MaskedBSgenome</w>
-      <w>MassOfArchangels</w>
-      <w>MatchGeneName</w>
-      <w>MatchedAssayExperiment</w>
-      <w>Matern</w>
-      <w>Matern.cor.to.range</w>
-      <w>MaternGLS.test</w>
-      <w>MaternGLSProfile.test</w>
-      <w>MaternQR.test</w>
-      <w>MaternQRProfile.test</w>
-      <w>Math</w>
-      <w>Math.Date</w>
-      <w>Math.POSIXt</w>
-      <w>Math.data.frame</w>
-      <w>Math.difftime</w>
-      <w>Math.factor</w>
-      <w>Math2</w>
-      <w>MathAchSchool</w>
-      <w>MathAchieve</w>
-      <w>Matrix</w>
-      <w>MatrixClass</w>
-      <w>MatrixModels</w>
-      <w>MatrixQuality</w>
-      <w>Mauritius</w>
-      <w>Mawson</w>
-      <w>Mayotte</w>
-      <w>Mazatlan</w>
-      <w>Mbabane</w>
-      <w>Mbox</w>
-      <w>McMurdo</w>
-      <w>Mchi</w>
-      <w>Mclust</w>
-      <w>MclustBootstrap</w>
-      <w>MclustDA</w>
-      <w>MclustDR</w>
-      <w>MclustDRrecoverdir</w>
-      <w>MclustDRsubsel</w>
-      <w>MclustDRsubsel1cycle</w>
-      <w>MclustDRsubsel_classif</w>
-      <w>MclustDRsubsel_cluster</w>
-      <w>Mean</w>
-      <w>MeanSD</w>
-      <w>Meat</w>
-      <w>MedUnits</w>
-      <w>Mehta</w>
-      <w>Melanoma</w>
-      <w>Melbourne</w>
-      <w>Mendoza</w>
-      <w>Menominee</w>
-      <w>Merge</w>
-      <w>Merida</w>
-      <w>Meta</w>
-      <w>MetaFeature</w>
-      <w>MethodAddCoerce</w>
-      <w>MethodsList</w>
-      <w>MethodsListSelect</w>
-      <w>MethylSet</w>
-      <w>MexicoCity</w>
-      <w>Mexico_City</w>
-      <w>Midway</w>
-      <w>Migration</w>
-      <w>Milk</w>
-      <w>MinMax</w>
-      <w>Minsk</w>
-      <w>Miquelon</w>
-      <w>Misc</w>
-      <w>Missing</w>
-      <w>Miwa</w>
-      <w>MixingMetric</w>
-      <w>Mod</w>
-      <w>Model</w>
-      <w>ModelEnvFormula</w>
-      <w>ModelEnvMatrix</w>
-      <w>ModelMetrics</w>
-      <w>Module</w>
-      <w>Mogadishu</w>
-      <w>Monaco</w>
-      <w>Moncton</w>
-      <w>Monrovia</w>
-      <w>Monterrey</w>
-      <w>Montevideo</w>
-      <w>Monticello</w>
-      <w>Montreal</w>
-      <w>Montserrat</w>
-      <w>Moore</w>
-      <w>Moran</w>
-      <w>Moran.I</w>
-      <w>MoranLocal</w>
-      <w>Moscow</w>
-      <w>MotifDb.Hsap</w>
-      <w>MotifDb.Hsap.PFM</w>
-      <w>MplsDemo</w>
-      <w>MplsStops</w>
-      <w>Mpsi</w>
-      <w>MrhoInf</w>
-      <w>Mroz</w>
-      <w>MsetEx</w>
-      <w>MsetEx.sub</w>
-      <w>MultiAssayExperiment</w>
-      <w>MultiGraph</w>
-      <w>MultiVerbose</w>
-      <w>MulticoreFuture</w>
-      <w>MulticoreParam</w>
-      <w>MultiprocessFuture</w>
-      <w>MultisessionFuture</w>
-      <w>Muscat</w>
-      <w>Muscle</w>
-      <w>Mwgt</w>
-      <w>MySQL</w>
-      <w>N50</w>
-      <w>N90</w>
-      <w>NA2x</w>
-      <w>NATURAL_INTRON_MOTIFS</w>
-      <w>NAToUnknown</w>
-      <w>NA_LLint_</w>
-      <w>NAvalue</w>
-      <w>NCBICHIP_DB_SeedGenerator</w>
-      <w>NCBI_snp_query</w>
-      <w>NCBI_snp_query2</w>
-      <w>NCG_EXTID2PATHID</w>
-      <w>NCG_PATHID2EXTID</w>
-      <w>NCG_PATHID2NAME</w>
-      <w>NCList</w>
-      <w>NCLists</w>
-      <w>NCOL</w>
-      <w>NChannelSet</w>
-      <w>NChannelSetToMethyLumiSet</w>
-      <w>NChannelSetToMethyLumiSet2</w>
-      <w>NHANES</w>
-      <w>NLSstAsymptotic</w>
-      <w>NLSstClosestX</w>
-      <w>NLSstLfAsymptote</w>
-      <w>NLSstRtAsymptote</w>
-      <w>NNMF</w>
-      <w>NNclean</w>
-      <w>NOBASEFIX</w>
-      <w>NOBLANKS</w>
-      <w>NOCDATA</w>
-      <w>NODICT</w>
-      <w>NOENT</w>
-      <w>NOERROR</w>
-      <w>NONET</w>
-      <w>NOWARNING</w>
-      <w>NOXINCNODE</w>
-      <w>NOdata</w>
-      <w>NOxEmissions</w>
-      <w>NP2009code</w>
-      <w>NPreg</w>
-      <w>NR</w>
-      <w>NROW</w>
-      <w>NS</w>
-      <w>NSBS</w>
-      <w>NSCLEAN</w>
-      <w>NSS.JD</w>
-      <w>NSS.SD</w>
-      <w>NSS.TD.JD</w>
-      <w>Nairobi</w>
-      <w>Name</w>
-      <w>Names</w>
-      <w>Names2names</w>
-      <w>Nassau</w>
-      <w>Nauru</w>
-      <w>Nclus</w>
-      <w>Ndists</w>
-      <w>Ndjamena</w>
-      <w>Nedge</w>
-      <w>Nedge.evonet</w>
-      <w>Nedge.multiPhylo</w>
-      <w>Nedge.phylo</w>
-      <w>Negate</w>
-      <w>Nethvote</w>
-      <w>NewChrBandTree</w>
-      <w>NewObject</w>
-      <w>NewYearsDay</w>
-      <w>NewYork</w>
-      <w>New_Salem</w>
-      <w>New_York</w>
-      <w>NextMethod</w>
-      <w>Niamey</w>
-      <w>Nicosia</w>
-      <w>Nile</w>
-      <w>Nipigon</w>
-      <w>Nitrendipene</w>
-      <w>Niue</w>
-      <w>Nnode</w>
-      <w>Nnode.multiPhylo</w>
-      <w>Nnode.phylo</w>
-      <w>NoAxes</w>
-      <w>NoGrid</w>
-      <w>NoLegend</w>
-      <w>Nome</w>
-      <w>Norfolk</w>
-      <w>NormalizeData</w>
-      <w>Noronha</w>
-      <w>Nouakchott</w>
-      <w>Noumea</w>
-      <w>Novosibirsk</w>
-      <w>NregFix</w>
-      <w>Ntip</w>
-      <w>Ntip.multiPhylo</w>
-      <w>Ntip.phylo</w>
-      <w>Null</w>
-      <w>NullCollection</w>
-      <w>NullIdentifier</w>
-      <w>NullVerbose</w>
-      <w>NumericList</w>
-      <w>NumericQuality</w>
-      <w>OBOCollection</w>
-      <w>OBOCollectionDatPkg</w>
-      <w>OBOHyperGParams</w>
-      <w>OBrienKaiser</w>
-      <w>OLD10</w>
-      <w>OLDSAX</w>
-      <w>OME</w>
-      <w>OMIMCollection</w>
-      <w>ONEwise</w>
-      <w>OR</w>
-      <w>ORDER</w>
-      <w>ORDER.default</w>
-      <w>OUT</w>
-      <w>Oats</w>
-      <w>Object</w>
-      <w>OldWhichCells</w>
-      <w>Ollerenshaw</w>
-      <w>OlsonNames</w>
-      <w>Omsk</w>
-      <w>OnDiskLongTable</w>
-      <w>OnDiskLongTable_old</w>
-      <w>One2One</w>
-      <w>OnlyCodingTxFilter</w>
-      <w>Ontology</w>
-      <w>Ops</w>
-      <w>Ops.CompressedMatrix</w>
-      <w>Ops.Date</w>
-      <w>Ops.POSIXt</w>
-      <w>Ops.data.frame</w>
-      <w>Ops.difftime</w>
-      <w>Ops.factor</w>
-      <w>Ops.matrix.csr</w>
-      <w>Ops.matrix.diag.csr</w>
-      <w>Ops.numeric_version</w>
-      <w>Ops.ordered</w>
-      <w>OptionParser</w>
-      <w>OptionParserOption</w>
-      <w>Options</w>
-      <w>OptionsManager</w>
-      <w>Oral</w>
-      <w>Orange</w>
-      <w>OrchardSprays</w>
-      <w>Ornstein</w>
-      <w>Orthodont</w>
-      <w>Oslo</w>
-      <w>OsloTransect</w>
-      <w>Other</w>
-      <w>Ouagadougou</w>
-      <w>Ovary</w>
-      <w>OverlayTrack</w>
-      <w>Oxboys</w>
-      <w>Oxide</w>
-      <w>PAM120</w>
-      <w>PAM250</w>
-      <w>PAM30</w>
-      <w>PAM40</w>
-      <w>PAM70</w>
-      <w>PATCH</w>
-      <w>PBG</w>
-      <w>PBmodcomp</w>
-      <w>PBmodcomp.lm</w>
-      <w>PBmodcomp.mer</w>
-      <w>PBmodcomp.merMod</w>
-      <w>PBrefdist</w>
-      <w>PBrefdist.lm</w>
-      <w>PBrefdist.mer</w>
-      <w>PBrefdist.merMod</w>
-      <w>PCA</w>
-      <w>PCAPlot</w>
-      <w>PCASigGenes</w>
-      <w>PCA_L1</w>
-      <w>PCAgrid</w>
-      <w>PCAproj</w>
-      <w>PCHeatmap</w>
-      <w>PCdiagplot</w>
-      <w>PD</w>
-      <w>PDict</w>
-      <w>PEDANTIC</w>
-      <w>PErisk</w>
-      <w>PFMtoPWM</w>
-      <w>PLtoGP</w>
-      <w>PMIDAmat</w>
-      <w>PMIDCollection</w>
-      <w>POST</w>
-      <w>PP.test</w>
-      <w>PRISMelevation</w>
-      <w>PSEA</w>
-      <w>PST</w>
-      <w>PUT</w>
-      <w>PValue</w>
-      <w>PWAmat</w>
-      <w>PWM</w>
-      <w>PWMCutoff4.hg19.MotifDb.Hsap</w>
-      <w>PWMCutoff5.hg19.MotifDb.Hsap</w>
-      <w>PWMEnrich</w>
-      <w>PWMEnrich.Hsapiens.background</w>
-      <w>PWMLogn.hg19.MotifDb.Hsap</w>
-      <w>PWMPvalueCutoff1e2.hg19.MotifDb.Hsap</w>
-      <w>PWMPvalueCutoff1e3.hg19.MotifDb.Hsap</w>
-      <w>PWMPvalueCutoff1e4.hg19.MotifDb.Hsap</w>
-      <w>PWMUnscaled</w>
-      <w>PWMscoreStartingAt</w>
-      <w>Pacific</w>
-      <w>Package</w>
-      <w>Paginator</w>
-      <w>Pago_Pago</w>
-      <w>Pairs</w>
-      <w>PairsBootOneRefFreeEwasModel</w>
-      <w>PairsBootRefFreeEwasModel</w>
-      <w>PairwiseAlignments</w>
-      <w>PairwiseAlignmentsSingleSubject</w>
-      <w>Palau</w>
-      <w>PalmSunday</w>
-      <w>Palmer</w>
-      <w>Panama</w>
-      <w>Pangnirtung</w>
-      <w>Paramaribo</w>
-      <w>Paris</w>
-      <w>ParseFormula</w>
-      <w>PartitioningByEnd</w>
-      <w>PartitioningByWidth</w>
-      <w>PartitioningMap</w>
-      <w>PatchStat</w>
-      <w>PathwayList</w>
-      <w>PcaClassic</w>
-      <w>PcaCov</w>
-      <w>PcaGrid</w>
-      <w>PcaHubert</w>
-      <w>PcaLocantore</w>
-      <w>PcaProj</w>
-      <w>Peirce</w>
-      <w>Pentecost</w>
-      <w>PentecostMonday</w>
-      <w>PercentAxis</w>
-      <w>PercentageFeatureSet</w>
-      <w>Perth</w>
-      <w>Petersburg</w>
-      <w>PfamCollection</w>
-      <w>Phenobarb</w>
-      <w>Phnom_Penh</w>
-      <w>Phoenix</w>
-      <w>Phonemes</w>
-      <w>PhredQuality</w>
-      <w>PileupFiles</w>
-      <w>PileupParam</w>
-      <w>Pima.te</w>
-      <w>Pima.tr</w>
-      <w>Pima.tr2</w>
-      <w>Pitcairn</w>
-      <w>Pixel</w>
-      <w>PlantGrowth</w>
-      <w>PlotClusterTree</w>
-      <w>Plots</w>
-      <w>Podgorica</w>
-      <w>PolyDimPlot</w>
-      <w>PolyFeaturePlot</w>
-      <w>PolySet2SpatialLines</w>
-      <w>PolySet2SpatialPolygons</w>
-      <w>Polygon</w>
-      <w>Polygons</w>
-      <w>Ponape</w>
-      <w>Pontianak</w>
-      <w>Port_Moresby</w>
-      <w>Port_of_Spain</w>
-      <w>Porto_Velho</w>
-      <w>Position</w>
-      <w>PositionDodge</w>
-      <w>PositionDodge2</w>
-      <w>PositionFill</w>
-      <w>PositionIdentity</w>
-      <w>PositionJitter</w>
-      <w>PositionJitterdodge</w>
-      <w>PositionNudge</w>
-      <w>PositionPointsJitter</w>
-      <w>PositionPointsSina</w>
-      <w>PositionRaincloud</w>
-      <w>PositionStack</w>
-      <w>PostProbMod</w>
-      <w>PostScriptTrace</w>
-      <w>Pottery</w>
-      <w>Prague</w>
-      <w>Predict</w>
-      <w>Predict.matrix</w>
-      <w>Predict.matrix.Bspline.smooth</w>
-      <w>Predict.matrix.cr.smooth</w>
-      <w>Predict.matrix.cs.smooth</w>
-      <w>Predict.matrix.cyclic.smooth</w>
-      <w>Predict.matrix.duchon.spline</w>
-      <w>Predict.matrix.gp.smooth</w>
-      <w>Predict.matrix.mrf.smooth</w>
-      <w>Predict.matrix.pspline.smooth</w>
-      <w>Predict.matrix.random.effect</w>
-      <w>Predict.matrix.sf</w>
-      <w>Predict.matrix.soap.film</w>
-      <w>Predict.matrix.sos.smooth</w>
-      <w>Predict.matrix.sw</w>
-      <w>Predict.matrix.t2.smooth</w>
-      <w>Predict.matrix.tensor.smooth</w>
-      <w>Predict.matrix.tprs.smooth</w>
-      <w>Predict.matrix.ts.smooth</w>
-      <w>Predict.matrix2</w>
-      <w>PredictMat</w>
-      <w>PresentationOfLord</w>
-      <w>Prestige</w>
-      <w>Procrustes</w>
-      <w>Progress</w>
-      <w>ProgressBar</w>
-      <w>Project</w>
-      <w>ProjectDim</w>
-      <w>Promax</w>
-      <w>PromoterVariants</w>
-      <w>PrositeCollection</w>
-      <w>ProtDomIdFilter</w>
-      <w>ProtGenerics</w>
-      <w>ProteinIdFilter</w>
-      <w>Psim</w>
-      <w>Puerto_Rico</w>
-      <w>Puromycin</w>
-      <w>PurpleAndYellow</w>
-      <w>Pyongyang</w>
-      <w>Q</w>
-      <w>QA</w>
-      <w>QAAdapterContamination</w>
-      <w>QACollate</w>
-      <w>QAData</w>
-      <w>QAFastqSource</w>
-      <w>QAFiltered</w>
-      <w>QAFlagged</w>
-      <w>QAFrequentSequence</w>
-      <w>QANucleotideByCycle</w>
-      <w>QANucleotideUse</w>
-      <w>QAQualityByCycle</w>
-      <w>QAQualityUse</w>
-      <w>QAReadQuality</w>
-      <w>QASequenceUse</w>
-      <w>QC.GUI</w>
-      <w>QCdata</w>
-      <w>QSreg</w>
-      <w>QTECox</w>
-      <w>QTps</w>
-      <w>QUnif</w>
-      <w>Q_NX</w>
-      <w>Q_global</w>
-      <w>Q_local</w>
-      <w>Qatar</w>
-      <w>QdaClassic</w>
-      <w>QdaCov</w>
-      <w>Qn</w>
-      <w>Qn.old</w>
-      <w>Qpenalty</w>
-      <w>QualityScaledAAStringSet</w>
-      <w>QualityScaledBStringSet</w>
-      <w>QualityScaledDNAStringSet</w>
-      <w>QualityScaledRNAStringSet</w>
-      <w>Quantile</w>
-      <w>Quantile2</w>
-      <w>Quartet</w>
-      <w>Quickload</w>
-      <w>QuickloadGenome</w>
-      <w>Quinidine</w>
-      <w>Quinquagesima</w>
-      <w>Quote</w>
-      <w>Qyzylorda</w>
-      <w>R</w>
-      <w>R.CMD</w>
-      <w>R.SHLIB</w>
-      <w>R.Version</w>
-      <w>R.exec</w>
-      <w>R.home</w>
-      <w>R.methodsS3</w>
-      <w>R.oo</w>
-      <w>R.utils</w>
-      <w>R.version</w>
-      <w>R.version.string</w>
-      <w>R1C1_to_A1</w>
-      <w>R2</w>
-      <w>R6</w>
-      <w>R6Class</w>
-      <w>RANN</w>
-      <w>RBGL</w>
-      <w>RBioinf_group</w>
-      <w>RCMexample</w>
-      <w>RColorBrewer</w>
-      <w>RCurl</w>
-      <w>RECOVER</w>
-      <w>REML.test</w>
-      <w>RETRY</w>
-      <w>RG.MA</w>
-      <w>RGB</w>
-      <w>RGChannelSet</w>
-      <w>RGChannelSetExtended</w>
-      <w>RGsetEx</w>
-      <w>RGsetEx.sub</w>
-      <w>RMSE</w>
-      <w>RMSEP</w>
-      <w>RMelevation</w>
-      <w>RMprecip</w>
-      <w>RMySQL</w>
-      <w>RNAMultipleAlignment</w>
-      <w>RNAString</w>
-      <w>RNAStringSet</w>
-      <w>RNAStringSetList</w>
-      <w>RNA_ALPHABET</w>
-      <w>RNA_BASES</w>
-      <w>RNA_GENETIC_CODE</w>
-      <w>RNG</w>
-      <w>RNGdigest</w>
-      <w>RNGinfo</w>
-      <w>RNGkind</w>
-      <w>RNGrecovery</w>
-      <w>RNGseed</w>
-      <w>RNGseq</w>
-      <w>RNGseq_seed</w>
-      <w>RNGstr</w>
-      <w>RNGtype</w>
-      <w>RNGversion</w>
-      <w>ROC</w>
-      <w>ROCR</w>
-      <w>ROCR.hiv</w>
-      <w>ROCR.simple</w>
-      <w>ROCR.xval</w>
-      <w>ROWNAMES</w>
-      <w>RPMM</w>
-      <w>RRBS</w>
-      <w>RSQLite</w>
-      <w>RShowDoc</w>
-      <w>RSiteSearch</w>
-      <w>RStudio_reprompt</w>
-      <w>RTdata</w>
-      <w>RTdata2</w>
-      <w>RUV1</w>
-      <w>RUV2</w>
-      <w>RUV4</w>
-      <w>RUVI</w>
-      <w>RUVIII</w>
-      <w>RUVadj</w>
-      <w>RUVfit</w>
-      <w>RUVinv</w>
-      <w>RUVrinv</w>
-      <w>RUnit</w>
-      <w>RVindex</w>
-      <w>R_NX</w>
-      <w>R_system_version</w>
-      <w>Rabbit</w>
-      <w>Rad.cov</w>
-      <w>Rad.image.cov</w>
-      <w>Rad.simple.cov</w>
-      <w>Radbound</w>
-      <w>RadialBasis</w>
-      <w>Rail</w>
-      <w>Rainy_River</w>
-      <w>RanEffdata</w>
-      <w>Range.lvm</w>
-      <w>RangedData</w>
-      <w>RangedRaggedAssay</w>
-      <w>RangedSelection</w>
-      <w>RangesList</w>
-      <w>Rangoon</w>
-      <w>Rankin_Inlet</w>
-      <w>Rarotonga</w>
-      <w>RatPupWeight</w>
-      <w>Ratio</w>
-      <w>RatioSet</w>
-      <w>Rattribnames</w>
-      <w>RawList</w>
-      <w>RccViolationException</w>
-      <w>Rcmd</w>
-      <w>Rcpp</w>
-      <w>Rcpp.package.skeleton</w>
-      <w>Rcpp.plugin.maker</w>
-      <w>RcppArmadillo</w>
-      <w>RcppArmadillo.package.skeleton</w>
-      <w>RcppEigen</w>
-      <w>RcppEigen.package.skeleton</w>
-      <w>RcppLdFlags</w>
-      <w>RcppProgress</w>
-      <w>RcppRoll</w>
-      <w>Rd2HTML</w>
-      <w>Rd2ex</w>
-      <w>Rd2latex</w>
-      <w>Rd2txt</w>
-      <w>Rd2txt_options</w>
-      <w>RdSection2latex</w>
-      <w>RdTextFilter</w>
-      <w>Rd_args</w>
-      <w>Rd_combo</w>
-      <w>Rd_db</w>
-      <w>Rd_fun</w>
-      <w>Rd_help2txt</w>
-      <w>Rd_name</w>
-      <w>Rd_title</w>
-      <w>RdaCollection</w>
-      <w>Rdapply</w>
-      <w>Rdiff</w>
-      <w>Rdindex</w>
-      <w>RdistC</w>
-      <w>Rdo2Rdf</w>
-      <w>Rdo_Rcode</w>
-      <w>Rdo_append_argument</w>
-      <w>Rdo_args2txt</w>
-      <w>Rdo_args2txt_list</w>
-      <w>Rdo_collect_aliases</w>
-      <w>Rdo_comment</w>
-      <w>Rdo_create</w>
-      <w>Rdo_drop_empty</w>
-      <w>Rdo_empty</w>
-      <w>Rdo_empty_sections</w>
-      <w>Rdo_fetch</w>
-      <w>Rdo_flatinsert</w>
-      <w>Rdo_flatremove</w>
-      <w>Rdo_get_arg</w>
-      <w>Rdo_get_args</w>
-      <w>Rdo_get_argument_names</w>
-      <w>Rdo_get_insert_pos</w>
-      <w>Rdo_get_item_labels</w>
-      <w>Rdo_insert</w>
-      <w>Rdo_insert_element</w>
-      <w>Rdo_is_newline</w>
-      <w>Rdo_item</w>
-      <w>Rdo_locate</w>
-      <w>Rdo_locate_core_section</w>
-      <w>Rdo_locate_leaves</w>
-      <w>Rdo_macro</w>
-      <w>Rdo_macro1</w>
-      <w>Rdo_macro2</w>
-      <w>Rdo_modify</w>
-      <w>Rdo_modify_simple</w>
-      <w>Rdo_newline</w>
-      <w>Rdo_piece_types</w>
-      <w>Rdo_piecetag</w>
-      <w>Rdo_predefined_sections</w>
-      <w>Rdo_remove_srcref</w>
-      <w>Rdo_reparse</w>
-      <w>Rdo_replace_section</w>
-      <w>Rdo_section</w>
-      <w>Rdo_sections</w>
-      <w>Rdo_sectype</w>
-      <w>Rdo_set_sectag</w>
-      <w>Rdo_set_section</w>
-      <w>Rdo_show</w>
-      <w>Rdo_sigitem</w>
-      <w>Rdo_tag</w>
-      <w>Rdo_tags</w>
-      <w>Rdo_text</w>
-      <w>Rdo_verb</w>
-      <w>Rdo_which</w>
-      <w>Rdo_which_tag_eq</w>
-      <w>Rdo_which_tag_in</w>
-      <w>Rdoc</w>
-      <w>RdocException</w>
-      <w>Rdpack</w>
-      <w>Rdpack_bibstyles</w>
-      <w>Rdreplace_section</w>
-      <w>Rdtagapply</w>
-      <w>Re</w>
-      <w>Read10X</w>
-      <w>Read10X_h5</w>
-      <w>ReadAffy</w>
-      <w>ReadAlevin</w>
-      <w>ReadAlevinCsv</w>
-      <w>ReadH5AD</w>
-      <w>Realdata</w>
-      <w>Recall</w>
-      <w>Recife</w>
-      <w>Recode</w>
-      <w>Reduce</w>
-      <w>RefFreeCellMix</w>
-      <w>RefFreeCellMixArray</w>
-      <w>RefFreeCellMixArrayDevianceBoot</w>
-      <w>RefFreeCellMixArrayDevianceBoots</w>
-      <w>RefFreeCellMixArrayWithCustomStart</w>
-      <w>RefFreeCellMixInitialize</w>
-      <w>RefFreeCellMixInitializeBySVD</w>
-      <w>RefFreeEWAS</w>
-      <w>RefFreeEwasModel</w>
-      <w>RefseqIdentifier</w>
-      <w>RegBest</w>
-      <w>Regina</w>
-      <w>Rehnquist</w>
-      <w>Reise</w>
-      <w>RelativeCounts</w>
-      <w>Relaxin</w>
-      <w>Remifentanil</w>
-      <w>RenameCells</w>
-      <w>RenameIdents</w>
-      <w>Rencoding</w>
-      <w>ReorderIdent</w>
-      <w>Resolute</w>
-      <w>RestoreLegend</w>
-      <w>Reunion</w>
-      <w>Reykjavik</w>
-      <w>Rgraphviz</w>
-      <w>Rgshhs</w>
-      <w>Rhdf5lib</w>
-      <w>Rhtslib</w>
-      <w>RidgePlot</w>
-      <w>Riga</w>
-      <w>Rio_Branco</w>
-      <w>Rio_Gallegos</w>
-      <w>Riyadh</w>
-      <w>Rkeyname</w>
-      <w>Rkeys</w>
-      <w>Rle</w>
-      <w>RleArray</w>
-      <w>RleList</w>
-      <w>RleViewsList</w>
-      <w>Rlength</w>
-      <w>Rlogo</w>
-      <w>Rnjunc</w>
-      <w>Robey</w>
-      <w>RochePath</w>
-      <w>RocheSet</w>
-      <w>RodFramedata</w>
-      <w>Roffset</w>
-      <w>RogationSunday</w>
-      <w>Rome</w>
-      <w>Rossi</w>
-      <w>RotatedAxis</w>
-      <w>Rothera</w>
-      <w>Rows</w>
-      <w>Rprof</w>
-      <w>Rprofmem</w>
-      <w>Rrank</w>
-      <w>Rsamtools</w>
-      <w>Rscript</w>
-      <w>RtaIntensity</w>
-      <w>Rtangle</w>
-      <w>RtangleSetup</w>
-      <w>RtangleWritedoc</w>
-      <w>Rtsne</w>
-      <w>Rtsne_neighbors</w>
-      <w>Rubber</w>
-      <w>RunALRA</w>
-      <w>RunCCA</w>
-      <w>RunICA</w>
-      <w>RunLSI</w>
-      <w>RunPCA</w>
-      <w>RunTSNE</w>
-      <w>RunUMAP</w>
-      <w>Rversion</w>
-      <w>RweaveChunkPrefix</w>
-      <w>RweaveEvalWithOpt</w>
-      <w>RweaveLatex</w>
-      <w>RweaveLatexFinish</w>
-      <w>RweaveLatexOptions</w>
-      <w>RweaveLatexSetup</w>
-      <w>RweaveLatexWritedoc</w>
-      <w>RweaveTryStop</w>
-      <w>S</w>
-      <w>S3Class</w>
-      <w>S3Part</w>
-      <w>S4Vectors</w>
-      <w>S4formals</w>
-      <w>SAX1</w>
-      <w>SC3</w>
-      <w>SCB</w>
-      <w>SCCellSpace</w>
-      <w>SCFlu</w>
-      <w>SCLabels</w>
-      <w>SCTransform</w>
-      <w>SD</w>
-      <w>SDM</w>
-      <w>SDMTools</w>
-      <w>SFastqQuality</w>
-      <w>SIGCHLD</w>
-      <w>SIGCONT</w>
-      <w>SIGHUP</w>
-      <w>SIGINT</w>
-      <w>SIGKILL</w>
-      <w>SIGQUIT</w>
-      <w>SIGSTOP</w>
-      <w>SIGTERM</w>
-      <w>SIGTSTP</w>
-      <w>SIGUSR1</w>
-      <w>SIGUSR2</w>
-      <w>SIR</w>
-      <w>SJ</w>
-      <w>SLC14_1</w>
-      <w>SLC14_2</w>
-      <w>SLID</w>
-      <w>SNP_LOC_DATA</w>
-      <w>SNPlocs_pkgname</w>
-      <w>SNPs.132CommonSingle</w>
-      <w>SNPs.135CommonSingle</w>
-      <w>SNPs.137CommonSingle</w>
-      <w>SNPs.138CommonSingle</w>
-      <w>SNPs.141CommonSingle</w>
-      <w>SNPs.142CommonSingle</w>
-      <w>SNPs.144CommonSingle</w>
-      <w>SNPs.146CommonSingle</w>
-      <w>SNPs.147CommonSingle</w>
-      <w>SNPs.Illumina</w>
-      <w>SOBI</w>
-      <w>SOM</w>
-      <w>SP500</w>
-      <w>SQL</w>
-      <w>SQLITE_RO</w>
-      <w>SQLITE_RW</w>
-      <w>SQLITE_RWC</w>
-      <w>SQLKeywords</w>
-      <w>SQLite</w>
-      <w>SQUAREM</w>
-      <w>SRError</w>
-      <w>SRFilterResult</w>
-      <w>SRList</w>
-      <w>SRVector</w>
-      <w>SRWarn</w>
-      <w>SSD</w>
-      <w>SSI</w>
-      <w>SSLVERSION_DEFAULT</w>
-      <w>SSLVERSION_LAST</w>
-      <w>SSLVERSION_SSLv2</w>
-      <w>SSLVERSION_SSLv3</w>
-      <w>SSLVERSION_TLSv1</w>
-      <w>SSVSquantreg</w>
-      <w>SSasymp</w>
-      <w>SSasympOff</w>
-      <w>SSasympOrig</w>
-      <w>SSbiexp</w>
-      <w>SSfol</w>
-      <w>SSfpl</w>
-      <w>SSgompertz</w>
-      <w>SSlogis</w>
-      <w>SSmicmen</w>
-      <w>SSweibull</w>
-      <w>SVDwithMissing</w>
-      <w>SVindex</w>
-      <w>SW</w>
-      <w>SWAN</w>
-      <w>SWAN.MethyLumiSet</w>
-      <w>SWAN.RGChannelSet</w>
-      <w>SWAN.default</w>
-      <w>Sacramento</w>
-      <w>Sahlins</w>
-      <w>Saigon</w>
-      <w>Saipan</w>
-      <w>Sakhalin</w>
-      <w>Salaries</w>
-      <w>Samara</w>
-      <w>Samarkand</w>
-      <w>SampleName</w>
-      <w>SampleUMI</w>
-      <w>San_Juan</w>
-      <w>San_Marino</w>
-      <w>Santiago</w>
-      <w>Santo_Domingo</w>
-      <w>Sao_Paulo</w>
-      <w>Sao_Tome</w>
-      <w>Sarajevo</w>
-      <w>Save</w>
-      <w>Scale</w>
-      <w>ScaleAdv</w>
-      <w>ScaleContinuous</w>
-      <w>ScaleContinuousDate</w>
-      <w>ScaleContinuousDatetime</w>
-      <w>ScaleContinuousIdentity</w>
-      <w>ScaleContinuousPosition</w>
-      <w>ScaleCyclical</w>
-      <w>ScaleData</w>
-      <w>ScaleDiscrete</w>
-      <w>ScaleDiscreteIdentity</w>
-      <w>ScaleDiscretePosition</w>
-      <w>Scalebar</w>
-      <w>ScanBamParam</w>
-      <w>ScanBcfParam</w>
-      <w>ScanVcfParam</w>
-      <w>Schmid</w>
-      <w>Schur</w>
-      <w>Schutz</w>
-      <w>ScoreJackStraw</w>
-      <w>Scoresbysund</w>
-      <w>SeatacWeather</w>
-      <w>Seatbelts</w>
-      <w>Secondary</w>
-      <w>SelectIntegrationFeatures</w>
-      <w>SelfHits</w>
-      <w>Senate</w>
-      <w>Seoul</w>
-      <w>Septuagesima</w>
-      <w>SeqNameFilter</w>
-      <w>SeqStrandFilter</w>
-      <w>SeqendFilter</w>
-      <w>Seqinfo</w>
-      <w>SeqinfoForBSGenome</w>
-      <w>SeqinfoForUCSCGenome</w>
-      <w>SeqnameFilter</w>
-      <w>SeqstartFilter</w>
-      <w>SeqstrandFilter</w>
-      <w>SequenceTrack</w>
-      <w>SequentialFuture</w>
-      <w>SerialParam</w>
-      <w>SetAssayData</w>
-      <w>SetIdent</w>
-      <w>SetIntegrationData</w>
-      <w>Settings</w>
-      <w>Seurat</w>
-      <w>SeuratAxes</w>
-      <w>SeuratTheme</w>
-      <w>Shanghai</w>
-      <w>SharedData</w>
-      <w>SharedRaw</w>
-      <w>SharedRaw.read</w>
-      <w>SharedRaw.readComplexes</w>
-      <w>SharedRaw.readInts</w>
-      <w>SharedRaw.write</w>
-      <w>SharedRaw.writeInts</w>
-      <w>SharedVector.compare</w>
-      <w>SharedVector.copy</w>
-      <w>Shepard</w>
-      <w>Shiprock</w>
-      <w>ShortRead</w>
-      <w>ShortReadQ</w>
-      <w>SideEffectChunkCallback</w>
-      <w>SiegelsEx</w>
-      <w>SigDiff</w>
-      <w>SignatureMethod</w>
-      <w>SimCompRisk</w>
-      <w>SimSurv</w>
-      <w>Simferopol</w>
-      <w>SimpleList</w>
-      <w>Singapore</w>
-      <w>SingleCellExperiment</w>
-      <w>Sitka</w>
-      <w>Sitka89</w>
-      <w>Skopje</w>
-      <w>Skye</w>
-      <w>Sl.initial.repara</w>
-      <w>Sl.repara</w>
-      <w>Sl.setup</w>
-      <w>SmartComments</w>
-      <w>SmartControl</w>
-      <w>Smithsonian</w>
-      <w>Smoking</w>
-      <w>Sn</w>
-      <w>Snapshot</w>
-      <w>SnapshotFunction</w>
-      <w>SnapshotFunctionList</w>
-      <w>SnowParam</w>
-      <w>Sobj_SpatialGrid</w>
-      <w>Sofia</w>
-      <w>Soils</w>
-      <w>SolemnityOfMary</w>
-      <w>SolexaIntensity</w>
-      <w>SolexaIntensityInfo</w>
-      <w>SolexaPath</w>
-      <w>SolexaQuality</w>
-      <w>SolexaSet</w>
-      <w>South_Georgia</w>
-      <w>South_Pole</w>
-      <w>Soybean</w>
-      <w>SpExtent</w>
-      <w>SpPoly</w>
-      <w>SpPolyPart</w>
-      <w>SpPolygons</w>
-      <w>SpTrellis</w>
-      <w>SparseDeltas</w>
-      <w>SparseM</w>
-      <w>Spatial</w>
-      <w>SpatialGrid</w>
-      <w>SpatialGridDataFrame</w>
-      <w>SpatialLines</w>
-      <w>SpatialLines2PolySet</w>
-      <w>SpatialLines2map</w>
-      <w>SpatialLinesDataFrame</w>
-      <w>SpatialLinesLengths</w>
-      <w>SpatialLinesMidPoints</w>
-      <w>SpatialMultiPoints</w>
-      <w>SpatialMultiPointsDataFrame</w>
-      <w>SpatialPixels</w>
-      <w>SpatialPixelsDataFrame</w>
-      <w>SpatialPoints</w>
-      <w>SpatialPointsDataFrame</w>
-      <w>SpatialPolygons</w>
-      <w>SpatialPolygons2PolySet</w>
-      <w>SpatialPolygons2map</w>
-      <w>SpatialPolygonsDataFrame</w>
-      <w>SpatialPolygonsRescale</w>
-      <w>SpatialTheme</w>
-      <w>Specials</w>
-      <w>SpikeIn</w>
-      <w>SplashDams</w>
-      <w>SpliceSiteVariants</w>
-      <w>SplitDataFrameList</w>
-      <w>SplitObject</w>
-      <w>Spruce</w>
-      <w>St_Barthelemy</w>
-      <w>St_Helena</w>
-      <w>St_Johns</w>
-      <w>St_Kitts</w>
-      <w>St_Lucia</w>
-      <w>St_Thomas</w>
-      <w>St_Vincent</w>
-      <w>StanHeaders</w>
-      <w>Stangle</w>
-      <w>Stanley</w>
-      <w>StashIdent</w>
-      <w>Stat</w>
-      <w>StatBin</w>
-      <w>StatBin2d</w>
-      <w>StatBindot</w>
-      <w>StatBinhex</w>
-      <w>StatBinline</w>
-      <w>StatBoxplot</w>
-      <w>StatContour</w>
-      <w>StatCount</w>
-      <w>StatDensity</w>
-      <w>StatDensity2d</w>
-      <w>StatDensityRidges</w>
-      <w>StatEcdf</w>
-      <w>StatEllipse</w>
-      <w>StatFunction</w>
-      <w>StatIdentity</w>
-      <w>StatPlsmo</w>
-      <w>StatQq</w>
-      <w>StatQqLine</w>
-      <w>StatQuantile</w>
-      <w>StatSf</w>
-      <w>StatSfCoordinates</w>
-      <w>StatSmooth</w>
-      <w>StatSum</w>
-      <w>StatSummary</w>
-      <w>StatSummary2d</w>
-      <w>StatSummaryBin</w>
-      <w>StatSummaryHex</w>
-      <w>StatUnique</w>
-      <w>StatYdensity</w>
-      <w>States</w>
-      <w>Stdev</w>
-      <w>Stockholm</w>
-      <w>StopCellbrowser</w>
-      <w>Strauss</w>
-      <w>StructTS</w>
-      <w>SubsetByBarcodeInflections</w>
-      <w>SubsetData</w>
-      <w>SummarizedExperiment</w>
-      <w>Summary</w>
-      <w>Summary.Date</w>
-      <w>Summary.POSIXct</w>
-      <w>Summary.POSIXlt</w>
-      <w>Summary.data.frame</w>
-      <w>Summary.difftime</w>
-      <w>Summary.factor</w>
-      <w>Summary.numeric_version</w>
-      <w>Summary.ordered</w>
-      <w>SupremeCourt</w>
-      <w>Surv</w>
-      <w>Sweave</w>
-      <w>Sweave2knitr</w>
-      <w>SweaveHooks</w>
-      <w>SweaveSyntConv</w>
-      <w>SweaveSyntaxLatex</w>
-      <w>SweaveSyntaxNoweb</w>
-      <w>SweaveTeXFilter</w>
-      <w>Swift_Current</w>
-      <w>Sydney</w>
-      <w>SymbolFilter</w>
-      <w>SymbolIdentifier</w>
-      <w>Synonym</w>
-      <w>Syowa</w>
-      <w>Sys.Date</w>
-      <w>Sys.MIPS</w>
-      <w>Sys.chmod</w>
-      <w>Sys.cpuinfo</w>
-      <w>Sys.getenv</w>
-      <w>Sys.getenv_value</w>
-      <w>Sys.getlocale</w>
-      <w>Sys.getpid</w>
-      <w>Sys.glob</w>
-      <w>Sys.info</w>
-      <w>Sys.localeconv</w>
-      <w>Sys.memGB</w>
-      <w>Sys.meminfo</w>
-      <w>Sys.ps</w>
-      <w>Sys.ps.cmd</w>
-      <w>Sys.readlink</w>
-      <w>Sys.readlink2</w>
-      <w>Sys.setFileTime</w>
-      <w>Sys.setenv</w>
-      <w>Sys.setlocale</w>
-      <w>Sys.sizes</w>
-      <w>Sys.sleep</w>
-      <w>Sys.time</w>
-      <w>Sys.timeDate</w>
-      <w>Sys.timezone</w>
-      <w>Sys.umask</w>
-      <w>Sys.unsetenv</w>
-      <w>Sys.which</w>
-      <w>Sys.yearmon</w>
-      <w>Sys.yearqtr</w>
-      <w>System</w>
-      <w>T</w>
-      <w>T.Owen</w>
-      <w>T2.test</w>
-      <w>T2graph</w>
-      <w>TA.plot</w>
-      <w>TF.IDF</w>
-      <w>TFMLazyScore</w>
-      <w>TFMPvalue</w>
-      <w>TFMpv2sc</w>
-      <w>TFMsc2pv</w>
-      <w>TSNEPlot</w>
-      <w>TT</w>
-      <w>TVPACK</w>
-      <w>TabixFile</w>
-      <w>TabixFileList</w>
-      <w>Table</w>
-      <w>Tahiti</w>
-      <w>Taipei</w>
-      <w>Tal.Or</w>
-      <w>Tal_Or</w>
-      <w>Tallinn</w>
-      <w>Tapply</w>
-      <w>Tarawa</w>
-      <w>TargetQ</w>
-      <w>Tashkent</w>
-      <w>Tbilisi</w>
-      <w>TeX</w>
-      <w>Tegucigalpa</w>
-      <w>Tehran</w>
-      <w>Tell_City</w>
-      <w>Term</w>
-      <w>Tetracycline1</w>
-      <w>Tetracycline2</w>
-      <w>TextStatusBar</w>
-      <w>Theoph</w>
-      <w>Thimphu</w>
-      <w>ThreeUTRVariants</w>
-      <w>Thule</w>
-      <w>Thunder_Bay</w>
-      <w>Thurstone</w>
-      <w>Thurstone.33</w>
-      <w>Thurstone.9</w>
-      <w>Tijuana</w>
-      <w>TimeoutException</w>
-      <w>Tirane</w>
-      <w>Titanic</w>
-      <w>TitanicSurvival</w>
-      <w>Token</w>
-      <w>Token1.0</w>
-      <w>Token2.0</w>
-      <w>TokenServiceAccount</w>
-      <w>Tokyo</w>
-      <w>Tongatapu</w>
-      <w>Tool</w>
-      <w>ToothGrowth</w>
-      <w>TopCells</w>
-      <w>TopFeatures</w>
-      <w>Toronto</w>
-      <w>Tortola</w>
-      <w>Toydata</w>
-      <w>Tps</w>
-      <w>Traffic</w>
-      <w>Transact</w>
-      <w>TransferData</w>
-      <w>TransfigurationOfLord</w>
-      <w>TrinitySunday</w>
-      <w>Tripoli</w>
-      <w>Truk</w>
-      <w>Tucker</w>
-      <w>Tucuman</w>
-      <w>TukeyHSD</w>
-      <w>Tunis</w>
-      <w>Tweedie</w>
-      <w>TwoBitFile</w>
-      <w>TxBiotypeFilter</w>
-      <w>TxDb.Dmelanogaster.UCSC.dm3.ensGene</w>
-      <w>TxDb.Dmelanogaster.UCSC.dm6.ensGene</w>
-      <w>TxDb.Hsapiens.UCSC.hg19.knownGene</w>
-      <w>TxDb.Hsapiens.UCSC.hg38.knownGene</w>
-      <w>TxDb.Mmusculus.UCSC.mm10.knownGene</w>
-      <w>TxDb.Mmusculus.UCSC.mm9.knownGene</w>
-      <w>TxDb.Rnorvegicus.UCSC.rn4.ensGene</w>
-      <w>TxDb.Rnorvegicus.UCSC.rn5.refGene</w>
-      <w>TxDb.Rnorvegicus.UCSC.rn6.refGene</w>
-      <w>TxEndFilter</w>
-      <w>TxIdFilter</w>
-      <w>TxNameFilter</w>
-      <w>TxStartFilter</w>
-      <w>TxSupportLevelFilter</w>
-      <w>TxbiotypeFilter</w>
-      <w>TxidFilter</w>
-      <w>Type1Font</w>
-      <w>UCBAdmissions</w>
-      <w>UCSCFeatureDbTableSchema</w>
-      <w>UCSCFile</w>
-      <w>UKDriverDeaths</w>
-      <w>UKgas</w>
-      <w>UMAP</w>
-      <w>UMAPPlot</w>
-      <w>UN</w>
-      <w>UN98</w>
-      <w>URLdecode</w>
-      <w>URLencode</w>
-      <w>URLstring</w>
-      <w>US</w>
-      <w>US.dat</w>
-      <w>USAccDeaths</w>
-      <w>USAge.df</w>
-      <w>USAge.table</w>
-      <w>USArrests</w>
-      <w>USCPulaskisBirthday</w>
-      <w>USCancerRates</w>
-      <w>USChristmasDay</w>
-      <w>USColumbusDay</w>
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-      <w>USDecorationMemorialDay</w>
-      <w>USDistLag</w>
-      <w>USElectionDay</w>
-      <w>USGoodFriday</w>
-      <w>USInaugurationDay</w>
-      <w>USIndependenceDay</w>
-      <w>USJudgeRatings</w>
-      <w>USLaborDay</w>
-      <w>USLincolnsBirthday</w>
-      <w>USMLKingsBirthday</w>
-      <w>USMemorialDay</w>
-      <w>USMortality</w>
-      <w>USNewYearsDay</w>
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-      <w>USPop</w>
-      <w>USPresidentsDay</w>
-      <w>USRegionalMortality</w>
-      <w>USSouthPolygon</w>
-      <w>USThanksgivingDay</w>
-      <w>USVeteransDay</w>
-      <w>USWashingtonsBirthday</w>
-      <w>UScereal</w>
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-      <w>UScounties.ndorder</w>
-      <w>UScounties.storder</w>
-      <w>UScrime</w>
-      <w>USprecip</w>
-      <w>UcscTrack</w>
-      <w>Uhaz</w>
-      <w>Ulaanbaatar</w>
-      <w>UnexpectedFutureResultError</w>
-      <w>UniGeneQuery</w>
-      <w>UnigeneIdentifier</w>
-      <w>Union</w>
-      <w>UniprocessFuture</w>
-      <w>UniprotDbFilter</w>
-      <w>UniprotFilter</w>
-      <w>UniprotIdentifier</w>
-      <w>UniprotMappingTypeFilter</w>
-      <w>Unique</w>
-      <w>UpSetR</w>
-      <w>UpdateSeuratObject</w>
-      <w>Urumqi</w>
-      <w>UseFunction</w>
-      <w>UseMethod</w>
-      <w>Ushuaia</w>
-      <w>Uzhgorod</w>
-      <w>V</w>
-      <w>VA</w>
-      <w>VADeaths</w>
-      <w>VCF</w>
-      <w>VCFHeader</w>
-      <w>VComments</w>
-      <w>VDGN_EXTID2PATHID</w>
-      <w>VDGN_PATHID2EXTID</w>
-      <w>VDGN_PATHID2NAME</w>
-      <w>VERB</w>
-      <w>VRanges</w>
-      <w>VRangesList</w>
-      <w>VRangesScanVcfParam</w>
-      <w>VSS</w>
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-      <w>VSS.plot</w>
-      <w>VSS.scree</w>
-      <w>VSS.sim</w>
-      <w>VSS.simulate</w>
-      <w>VScount</w>
-      <w>Vaduz</w>
-      <w>Vancouver</w>
-      <w>VarCorr</w>
-      <w>VariableFeaturePlot</w>
-      <w>VariableFeatures</w>
-      <w>VariantAnnotation</w>
-      <w>Variogram</w>
-      <w>Vatican</w>
-      <w>VcfFile</w>
-      <w>VcfFileList</w>
-      <w>Vectorize</w>
-      <w>VennDiagram</w>
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-      <w>Vevay</w>
-      <w>Vienna</w>
-      <w>Vientiane</w>
-      <w>View</w>
-      <w>Views</w>
-      <w>Vilnius</w>
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-      <w>VizDimLoadings</w>
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-      <w>`!.bit`</w>
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-      <w>`.__T__AnnotatedDataFrame:Biobase`</w>
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-      <w>`.__T__ArrayWeights&lt;-:beadarray`</w>
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-      <w>`.__T__BIC:stats`</w>
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-      <w>`.__T__BunchKaufman:Matrix`</w>
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-      <w>`.__T__CNE21:CNEr`</w>
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-      <w>`.__T__CNEMerged:CNEr`</w>
-      <w>`.__T__CTSSclusteringMethod:CAGEr`</w>
-      <w>`.__T__CTSScoordinates:CAGEr`</w>
-      <w>`.__T__CTSSnormalizedTpm:CAGEr`</w>
-      <w>`.__T__CTSStagCount:CAGEr`</w>
-      <w>`.__T__Cholesky:Matrix`</w>
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-      <w>`.__T__Compare:methods`</w>
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-      <w>`.__T__ContrastMatrix&lt;-:beadarray`</w>
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-      <w>`.__T__Cy3&lt;-:methylumi`</w>
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-      <w>`.__T__Cy5&lt;-:methylumi`</w>
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-      <w>`.__T__DatPkgFactory:Category`</w>
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-      <w>`.__T__DesignMatrix:beadarray`</w>
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-      <w>`.__T__Detection:beadarray`</w>
-      <w>`.__T__Detection&lt;-:beadarray`</w>
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-      <w>`.__T__ExperimentList:MultiAssayExperiment`</w>
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-      <w>`.__T__FLXcheckComponent:flexmix`</w>
-      <w>`.__T__FLXdeterminePostunscaled:flexmix`</w>
-      <w>`.__T__FLXfit:flexmix`</w>
-      <w>`.__T__FLXgetDesign:flexmix`</w>
-      <w>`.__T__FLXgetK:flexmix`</w>
-      <w>`.__T__FLXgetModelmatrix:flexmix`</w>
-      <w>`.__T__FLXgetObs:flexmix`</w>
-      <w>`.__T__FLXgetParameters:flexmix`</w>
-      <w>`.__T__FLXgradlogLikfun:flexmix`</w>
-      <w>`.__T__FLXlogLikfun:flexmix`</w>
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-      <w>`.__T__FastqSamplerList:ShortRead`</w>
-      <w>`.__T__FastqStreamer:ShortRead`</w>
-      <w>`.__T__FastqStreamerList:ShortRead`</w>
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-      <w>`.__T__IQR:BiocGenerics`</w>
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-      <w>`.__T__KEGG2heatmap:annotate`</w>
-      <w>`.__T__KEGGFrame:AnnotationDbi`</w>
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-      <w>`.__T__KLdiv:modeltools`</w>
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-      <w>`.__T__Lkeys:AnnotationDbi`</w>
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-      <w>`.__T__Llength:AnnotationDbi`</w>
-      <w>`.__T__Loffset:GenomicAlignments`</w>
-      <w>`.__T__LogFC:beadarray`</w>
-      <w>`.__T__LogFC&lt;-:beadarray`</w>
-      <w>`.__T__LogOdds:beadarray`</w>
-      <w>`.__T__LogOdds&lt;-:beadarray`</w>
-      <w>`.__T__Logic:base`</w>
-      <w>`.__T__MAplot:affy`</w>
-      <w>`.__T__MAplot:lumi`</w>
-      <w>`.__T__MEapply:modeltools`</w>
-      <w>`.__T__MSbetween:quantro`</w>
-      <w>`.__T__MSwithin:quantro`</w>
-      <w>`.__T__Makesense:geneplotter`</w>
-      <w>`.__T__Map:BiocGenerics`</w>
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-      <w>`.__T__NROW:base`</w>
-      <w>`.__T__NSBS:S4Vectors`</w>
-      <w>`.__T__Name:topGO`</w>
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-      <w>`.__T__clusters:modeltools`</w>
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-      <w>`.__T__colFromX:raster`</w>
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-      <w>`.__T__columnMetadata&lt;-:IRanges`</w>
-      <w>`.__T__columns:AnnotationDbi`</w>
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-      <w>`.__T__combine:BiocGenerics`</w>
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-      <w>`.__T__combineNodes:graph`</w>
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-      <w>`.__T__complement:Biostrings`</w>
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-      <w>`.__T__computeAllFlinks:Biostrings`</w>
-      <w>`.__T__computeExprSet:affy`</w>
-      <w>`.__T__computeGeneSetsOverlap:GSVA`</w>
-      <w>`.__T__computeSpikeFactors:scran`</w>
-      <w>`.__T__computeSumFactors:scran`</w>
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-      <w>`.__T__conditional:Category`</w>
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-      <w>`.__T__conditions&lt;-:BiocGenerics`</w>
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-      <w>`.__T__consensusClusters:CAGEr`</w>
-      <w>`.__T__consensusClustersTpm:CAGEr`</w>
-      <w>`.__T__consensusMatrix:Biostrings`</w>
-      <w>`.__T__consensusString:Biostrings`</w>
-      <w>`.__T__consensusViews:Biostrings`</w>
-      <w>`.__T__consolidateTrack:Gviz`</w>
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-      <w>`.__T__contTable:topGO`</w>
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-      <w>`.__T__contributor&lt;-:GSEABase`</w>
-      <w>`.__T__controlData:methylumi`</w>
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-      <w>`.__T__convertFilter:AnnotationFilter`</w>
-      <w>`.__T__convertTo:scran`</w>
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-      <w>`.__T__coordinates&lt;-:sp`</w>
-      <w>`.__T__coordnames:sp`</w>
-      <w>`.__T__coordnames&lt;-:sp`</w>
-      <w>`.__T__coords:Gviz`</w>
-      <w>`.__T__coords:colorspace`</w>
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-      <w>`.__T__cor:stats`</w>
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-      <w>`.__T__cores:systemPipeR`</w>
-      <w>`.__T__corplot:methylumi`</w>
-      <w>`.__T__correlatePairs:scran`</w>
-      <w>`.__T__cos:base`</w>
-      <w>`.__T__cosh:base`</w>
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-      <w>`.__T__count.mappedLkeys:AnnotationDbi`</w>
-      <w>`.__T__count.mappedRkeys:AnnotationDbi`</w>
-      <w>`.__T__count.mappedkeys:AnnotationDbi`</w>
-      <w>`.__T__countBam:Rsamtools`</w>
-      <w>`.__T__countFa:Rsamtools`</w>
-      <w>`.__T__countGenesInTerm:topGO`</w>
-      <w>`.__T__countLines:ShortRead`</w>
-      <w>`.__T__countLnodeHits:S4Vectors`</w>
-      <w>`.__T__countMatches:S4Vectors`</w>
-      <w>`.__T__countOverlaps:IRanges`</w>
-      <w>`.__T__countPDict:Biostrings`</w>
-      <w>`.__T__countPWM:Biostrings`</w>
-      <w>`.__T__countPattern:Biostrings`</w>
-      <w>`.__T__countRnodeHits:S4Vectors`</w>
-      <w>`.__T__counts:BiocGenerics`</w>
-      <w>`.__T__counts&lt;-:BiocGenerics`</w>
-      <w>`.__T__cov2cor:stats`</w>
-      <w>`.__T__cov:stats`</w>
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-      <w>`.__T__covariates:IHW`</w>
-      <w>`.__T__cover:raster`</w>
-      <w>`.__T__coverage:IRanges`</w>
-      <w>`.__T__cpm:SingleCellExperiment`</w>
-      <w>`.__T__cpm&lt;-:SingleCellExperiment`</w>
-      <w>`.__T__creationDate:GSEABase`</w>
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-      <w>`.__T__crs:raster`</w>
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-      <w>`.__T__crunch:biovizBase`</w>
-      <w>`.__T__csi:kernlab`</w>
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-      <w>`.__T__cummin:base`</w>
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-      <w>`.__T__cumsum:base`</w>
-      <w>`.__T__cumulativeCTSSdistribution:CAGEr`</w>
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-      <w>`.__T__cutOff&lt;-:topGO`</w>
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-      <w>`.__T__danet:wateRmelon`</w>
-      <w>`.__T__dasen:wateRmelon`</w>
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-      <w>`.__T__dataTable:GEOquery`</w>
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-      <w>`.__T__dbGetPreparedQuery:RSQLite`</w>
-      <w>`.__T__dbGetQuery:DBI`</w>
-      <w>`.__T__dbGetRowCount:DBI`</w>
-      <w>`.__T__dbGetRowsAffected:DBI`</w>
-      <w>`.__T__dbGetStatement:DBI`</w>
-      <w>`.__T__dbHasCompleted:DBI`</w>
-      <w>`.__T__dbInfo:AnnotationDbi`</w>
-      <w>`.__T__dbIsReadOnly:DBI`</w>
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-      <w>`.__T__dbListConnections:DBI`</w>
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-      <w>`.__T__dbListResults:DBI`</w>
-      <w>`.__T__dbListTables:DBI`</w>
-      <w>`.__T__dbMoreResults:RMySQL`</w>
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-      <w>`.__T__dbQuoteIdentifier:DBI`</w>
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-      <w>`.__T__dbSendPreparedQuery:RSQLite`</w>
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-      <w>`.__T__dbSendStatement:DBI`</w>
-      <w>`.__T__dbSetDataMappings:DBI`</w>
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-      <w>`.__T__dbUnquoteIdentifier:DBI`</w>
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-      <w>`.__T__dbWriteTable:DBI`</w>
-      <w>`.__T__dbconn:BiocGenerics`</w>
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-      <w>`.__T__decode:S4Vectors`</w>
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-      <w>`.__T__dist_all_cdf:poweRlaw`</w>
-      <w>`.__T__dist_cdf:poweRlaw`</w>
-      <w>`.__T__dist_data_all_cdf:poweRlaw`</w>
-      <w>`.__T__dist_data_cdf:poweRlaw`</w>
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-      <w>`.__T__dist_rand:poweRlaw`</w>
-      <w>`.__T__distance:IRanges`</w>
-      <w>`.__T__distance:raster`</w>
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-      <w>`.__T__distance_to_nearest:intervals`</w>
-      <w>`.__T__distributeNegation:AnnotationFilter`</w>
-      <w>`.__T__dlogis:stats`</w>
-      <w>`.__T__dmrse:wateRmelon`</w>
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-      <w>`.__T__dmrse_row:wateRmelon`</w>
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-      <w>`.__T__edgeL:graph`</w>
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-      <w>`.__T__edgeSets:graph`</w>
-      <w>`.__T__edgeWeights:graph`</w>
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-      <w>`.__T__edgemode:graph`</w>
-      <w>`.__T__edgemode&lt;-:graph`</w>
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-      <w>`.__T__effectSize:Category`</w>
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-      <w>`.__T__elementMetadata:S4Vectors`</w>
-      <w>`.__T__elementMetadata&lt;-:S4Vectors`</w>
-      <w>`.__T__elementNROWS:S4Vectors`</w>
-      <w>`.__T__elementType:S4Vectors`</w>
-      <w>`.__T__elide:maptools`</w>
-      <w>`.__T__elim:topGO`</w>
-      <w>`.__T__elim&lt;-:topGO`</w>
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-      <w>`.__T__empty:modeltools`</w>
-      <w>`.__T__encodeOverlaps:GenomicAlignments`</w>
-      <w>`.__T__encoding:Biostrings`</w>
-      <w>`.__T__encodingHalves:GenomicAlignments`</w>
-      <w>`.__T__end:stats`</w>
-      <w>`.__T__end&lt;-:BiocGenerics`</w>
-      <w>`.__T__endElement.SAX:XML`</w>
-      <w>`.__T__endIndex:Biostrings`</w>
-      <w>`.__T__endoapply:S4Vectors`</w>
-      <w>`.__T__ensemblVersion:ensembldb`</w>
-      <w>`.__T__entityDeclaration.SAX:XML`</w>
-      <w>`.__T__ep:Rgraphviz`</w>
-      <w>`.__T__erase:raster`</w>
-      <w>`.__T__erode:hexbin`</w>
-      <w>`.__T__error:kernlab`</w>
-      <w>`.__T__esApply:Biobase`</w>
-      <w>`.__T__estimateCoverage:biovizBase`</w>
-      <w>`.__T__estimateDispersions:BiocGenerics`</w>
-      <w>`.__T__estimateSizeFactors:BiocGenerics`</w>
-      <w>`.__T__eval:BiocGenerics`</w>
-      <w>`.__T__evalSeparately:S4Vectors`</w>
-      <w>`.__T__evidenceCode:GSEABase`</w>
-      <w>`.__T__existGradient:flexmix`</w>
-      <w>`.__T__exists:base`</w>
-      <w>`.__T__exon:Gviz`</w>
-      <w>`.__T__exon&lt;-:Gviz`</w>
-      <w>`.__T__exons:GenomicFeatures`</w>
-      <w>`.__T__exonsBy:GenomicFeatures`</w>
-      <w>`.__T__exonsByOverlaps:GenomicFeatures`</w>
-      <w>`.__T__exp:base`</w>
-      <w>`.__T__expand.grid:S4Vectors`</w>
-      <w>`.__T__expand:Matrix`</w>
-      <w>`.__T__expand:S4Vectors`</w>
-      <w>`.__T__expand:intervals`</w>
-      <w>`.__T__expectedCounts:Category`</w>
-      <w>`.__T__experimentData:Biobase`</w>
-      <w>`.__T__experimentData&lt;-:Biobase`</w>
-      <w>`.__T__experimentPath:ShortRead`</w>
-      <w>`.__T__experiments:MultiAssayExperiment`</w>
-      <w>`.__T__experiments&lt;-:MultiAssayExperiment`</w>
-      <w>`.__T__expinfo:Biobase`</w>
-      <w>`.__T__expm:Matrix`</w>
-      <w>`.__T__export.2bit:rtracklayer`</w>
-      <w>`.__T__export.bed15:rtracklayer`</w>
-      <w>`.__T__export.bed:rtracklayer`</w>
-      <w>`.__T__export.bedGraph:rtracklayer`</w>
-      <w>`.__T__export.bw:rtracklayer`</w>
-      <w>`.__T__export.gff1:rtracklayer`</w>
-      <w>`.__T__export.gff2:rtracklayer`</w>
-      <w>`.__T__export.gff3:rtracklayer`</w>
-      <w>`.__T__export.gff:rtracklayer`</w>
-      <w>`.__T__export.ucsc:rtracklayer`</w>
-      <w>`.__T__export.wig:rtracklayer`</w>
-      <w>`.__T__export:rtracklayer`</w>
-      <w>`.__T__exportCTSStoBedGraph:CAGEr`</w>
-      <w>`.__T__exportToBed:CAGEr`</w>
-      <w>`.__T__exportToTabix:rtracklayer`</w>
-      <w>`.__T__express.summary.stat:affy`</w>
-      <w>`.__T__expressionClasses:CAGEr`</w>
-      <w>`.__T__expressionMatrix:topGO`</w>
-      <w>`.__T__exprs:Biobase`</w>
-      <w>`.__T__exprs&lt;-:Biobase`</w>
-      <w>`.__T__extend:raster`</w>
-      <w>`.__T__extent:raster`</w>
-      <w>`.__T__extract:raster`</w>
-      <w>`.__T__extract:rstan`</w>
-      <w>`.__T__extractAt:Biostrings`</w>
-      <w>`.__T__extractExpressionClass:CAGEr`</w>
-      <w>`.__T__extractFromTo:graph`</w>
-      <w>`.__T__extractList:IRanges`</w>
-      <w>`.__T__extractROWS:S4Vectors`</w>
-      <w>`.__T__extractSkippedExonRanks:GenomicAlignments`</w>
-      <w>`.__T__extractSpannedExonRanks:GenomicAlignments`</w>
-      <w>`.__T__extractSteppedExonRanks:GenomicAlignments`</w>
-      <w>`.__T__extractTranscriptSeqs:GenomicFeatures`</w>
-      <w>`.__T__extractUpstreamSeqs:GenomicFeatures`</w>
-      <w>`.__T__fData:Biobase`</w>
-      <w>`.__T__fData&lt;-:Biobase`</w>
-      <w>`.__T__fac:ShortRead`</w>
-      <w>`.__T__facmul:Matrix`</w>
-      <w>`.__T__factorNames:MOFAtools`</w>
-      <w>`.__T__factorNames&lt;-:MOFAtools`</w>
-      <w>`.__T__feasible:topGO`</w>
-      <w>`.__T__feasible&lt;-:topGO`</w>
-      <w>`.__T__feature:Gviz`</w>
-      <w>`.__T__feature&lt;-:Gviz`</w>
-      <w>`.__T__featureData:Biobase`</w>
-      <w>`.__T__featureData&lt;-:Biobase`</w>
-      <w>`.__T__featureFilter:methylumi`</w>
-      <w>`.__T__featureNames:Biobase`</w>
-      <w>`.__T__featureNames:MOFAtools`</w>
-      <w>`.__T__featureNames&lt;-:Biobase`</w>
-      <w>`.__T__featureNames&lt;-:MOFAtools`</w>
-      <w>`.__T__features:GenomicFeatures`</w>
-      <w>`.__T__fetch:DBI`</w>
-      <w>`.__T__field:AnnotationFilter`</w>
-      <w>`.__T__fileName:BiocGenerics`</w>
-      <w>`.__T__files:ShortRead`</w>
-      <w>`.__T__fillcolor:Rgraphviz`</w>
-      <w>`.__T__filt:VariantAnnotation`</w>
-      <w>`.__T__filt&lt;-:VariantAnnotation`</w>
-      <w>`.__T__filter:scater`</w>
-      <w>`.__T__filterBam:Rsamtools`</w>
-      <w>`.__T__filterGeneSets:GSVA`</w>
-      <w>`.__T__filterRules:S4Vectors`</w>
-      <w>`.__T__filterVcf:VariantAnnotation`</w>
-      <w>`.__T__finCenter:timeDate`</w>
-      <w>`.__T__finCenter&lt;-:timeDate`</w>
-      <w>`.__T__findCompatibleOverlaps:GenomicAlignments`</w>
-      <w>`.__T__findMarkers:scran`</w>
-      <w>`.__T__findMatches:S4Vectors`</w>
-      <w>`.__T__findOverlaps:IRanges`</w>
-      <w>`.__T__findPalindromes:Biostrings`</w>
-      <w>`.__T__findRange:IRanges`</w>
-      <w>`.__T__findRun:S4Vectors`</w>
-      <w>`.__T__findSpliceOverlaps:GenomicAlignments`</w>
-      <w>`.__T__first:S4Vectors`</w>
-      <w>`.__T__first&lt;-:S4Vectors`</w>
-      <w>`.__T__fit:modeltools`</w>
-      <w>`.__T__fitted.values:stats`</w>
-      <w>`.__T__fitted:stats`</w>
-      <w>`.__T__fiveUTRsByTranscript:GenomicFeatures`</w>
-      <w>`.__T__fixCoordinates:CNEr`</w>
-      <w>`.__T__fixed:VariantAnnotation`</w>
-      <w>`.__T__fixed&lt;-:VariantAnnotation`</w>
-      <w>`.__T__flag:ShortRead`</w>
-      <w>`.__T__flank:IRanges`</w>
-      <w>`.__T__flexmix:flexmix`</w>
-      <w>`.__T__flip:raster`</w>
-      <w>`.__T__flippedQuery:GenomicAlignments`</w>
-      <w>`.__T__floor:base`</w>
-      <w>`.__T__focal:raster`</w>
-      <w>`.__T__follow:IRanges`</w>
-      <w>`.__T__forceSymmetric:Matrix`</w>
-      <w>`.__T__forgeBSgenomeDataPkg:BSgenome`</w>
-      <w>`.__T__forgeMaskedBSgenomeDataPkg:BSgenome`</w>
-      <w>`.__T__formals&lt;-:base`</w>
-      <w>`.__T__format:base`</w>
-      <w>`.__T__formatDescription:rtracklayer`</w>
-      <w>`.__T__formula:stats`</w>
-      <w>`.__T__forwardsolve:base`</w>
-      <w>`.__T__forwardsolve:spam`</w>
-      <w>`.__T__fpkm:scater`</w>
-      <w>`.__T__fpkm&lt;-:scater`</w>
-      <w>`.__T__fragment&lt;-:urltools`</w>
-      <w>`.__T__free:XML`</w>
-      <w>`.__T__freq:raster`</w>
-      <w>`.__T__frequency:stats`</w>
-      <w>`.__T__from:Rgraphviz`</w>
-      <w>`.__T__from:S4Vectors`</w>
-      <w>`.__T__fromGXL:graph`</w>
-      <w>`.__T__fuks:wateRmelon`</w>
-      <w>`.__T__fullgrid:sp`</w>
-      <w>`.__T__fullgrid&lt;-:sp`</w>
-      <w>`.__T__functions:ShortRead`</w>
-      <w>`.__T__fvarLabels:Biobase`</w>
-      <w>`.__T__fvarLabels&lt;-:Biobase`</w>
-      <w>`.__T__fvarMetadata:Biobase`</w>
-      <w>`.__T__fvarMetadata&lt;-:Biobase`</w>
-      <w>`.__T__gamma:base`</w>
-      <w>`.__T__gaps:IRanges`</w>
-      <w>`.__T__gausspr:kernlab`</w>
-      <w>`.__T__gene:Gviz`</w>
-      <w>`.__T__gene&lt;-:Gviz`</w>
-      <w>`.__T__geneColor:GSEABase`</w>
-      <w>`.__T__geneColor&lt;-:GSEABase`</w>
-      <w>`.__T__geneCounts:Category`</w>
-      <w>`.__T__geneData:topGO`</w>
-      <w>`.__T__geneData&lt;-:topGO`</w>
-      <w>`.__T__geneIdType:GSEABase`</w>
-      <w>`.__T__geneIdType&lt;-:GSEABase`</w>
-      <w>`.__T__geneIdUniverse:Category`</w>
-      <w>`.__T__geneIds:GSEABase`</w>
-      <w>`.__T__geneIds&lt;-:GSEABase`</w>
-      <w>`.__T__geneIdsByCategory:Category`</w>
-      <w>`.__T__geneMappedCount:Category`</w>
-      <w>`.__T__geneNames:affy`</w>
-      <w>`.__T__geneScore:topGO`</w>
-      <w>`.__T__geneSelectionFun:topGO`</w>
-      <w>`.__T__geneSelectionFun&lt;-:topGO`</w>
-      <w>`.__T__geneSymbols:annotate`</w>
-      <w>`.__T__genefinder:genefilter`</w>
-      <w>`.__T__genes:GenomicFeatures`</w>
-      <w>`.__T__genes:topGO`</w>
-      <w>`.__T__genesInTerm:topGO`</w>
-      <w>`.__T__genki:wateRmelon`</w>
-      <w>`.__T__geno:VariantAnnotation`</w>
-      <w>`.__T__geno&lt;-:VariantAnnotation`</w>
-      <w>`.__T__genome:GenomeInfoDb`</w>
-      <w>`.__T__genome&lt;-:GenomeInfoDb`</w>
-      <w>`.__T__genomeName:CAGEr`</w>
-      <w>`.__T__genotypeToSnpMatrix:VariantAnnotation`</w>
-      <w>`.__T__geom:raster`</w>
-      <w>`.__T__geometry:sp`</w>
-      <w>`.__T__geometry&lt;-:sp`</w>
-      <w>`.__T__get:BiocGenerics`</w>
-      <w>`.__T__getBeta:minfi`</w>
-      <w>`.__T__getBimapFilters:AnnotationDbi`</w>
-      <w>`.__T__getCN:minfi`</w>
-      <w>`.__T__getCTSS:CAGEr`</w>
-      <w>`.__T__getCenter:rrcov`</w>
-      <w>`.__T__getCorr:rrcov`</w>
-      <w>`.__T__getCov:rrcov`</w>
-      <w>`.__T__getData:dimRed`</w>
-      <w>`.__T__getData:rrcov`</w>
-      <w>`.__T__getDataPart:methods`</w>
-      <w>`.__T__getDet:rrcov`</w>
-      <w>`.__T__getDimRedData:dimRed`</w>
-      <w>`.__T__getDistance:rrcov`</w>
-      <w>`.__T__getDynLib:inline`</w>
-      <w>`.__T__getEigenvalues:rrcov`</w>
-      <w>`.__T__getEncoding:XML`</w>
-      <w>`.__T__getEvals:rrcov`</w>
-      <w>`.__T__getExpressionProfiles:CAGEr`</w>
-      <w>`.__T__getFlag:rrcov`</w>
-      <w>`.__T__getGOFrameData:AnnotationDbi`</w>
-      <w>`.__T__getGaps:biovizBase`</w>
-      <w>`.__T__getGeneRegionTrackForGviz:ensembldb`</w>
-      <w>`.__T__getGenomeFaFile:ensembldb`</w>
-      <w>`.__T__getHMedian:hexbin`</w>
-      <w>`.__T__getHistory:lumi`</w>
-      <w>`.__T__getHistory:methylumi`</w>
-      <w>`.__T__getHub:AnnotationHub`</w>
-      <w>`.__T__getKEGGFrameData:AnnotationDbi`</w>
-      <w>`.__T__getListElement:S4Vectors`</w>
-      <w>`.__T__getLoadings:rrcov`</w>
-      <w>`.__T__getM:minfi`</w>
-      <w>`.__T__getManifest:minfi`</w>
-      <w>`.__T__getMeta:dimRed`</w>
-      <w>`.__T__getMeth:minfi`</w>
-      <w>`.__T__getMeth:rrcov`</w>
-      <w>`.__T__getModel:modeltools`</w>
-      <w>`.__T__getNDim:dimRed`</w>
-      <w>`.__T__getNodeCenter:Rgraphviz`</w>
-      <w>`.__T__getNodeHeight:Rgraphviz`</w>
-      <w>`.__T__getNodeLW:Rgraphviz`</w>
-      <w>`.__T__getNodeRW:Rgraphviz`</w>
-      <w>`.__T__getNodeXY:Rgraphviz`</w>
-      <w>`.__T__getOrgData:dimRed`</w>
-      <w>`.__T__getOtherData:dimRed`</w>
-      <w>`.__T__getPar:Gviz`</w>
-      <w>`.__T__getPars:dimRed`</w>
-      <w>`.__T__getPoints:Rgraphviz`</w>
-      <w>`.__T__getPrcomp:rrcov`</w>
-      <w>`.__T__getPromoterSeq:GenomicFeatures`</w>
-      <w>`.__T__getQuan:rrcov`</w>
-      <w>`.__T__getRNG1:rngtools`</w>
-      <w>`.__T__getRaw:rrcov`</w>
-      <w>`.__T__getScale:rrcov`</w>
-      <w>`.__T__getScores:rrcov`</w>
-      <w>`.__T__getSdev:rrcov`</w>
-      <w>`.__T__getSeq:Biostrings`</w>
-      <w>`.__T__getShape:rrcov`</w>
-      <w>`.__T__getShiftingPromoters:CAGEr`</w>
-      <w>`.__T__getSigGroups:topGO`</w>
-      <w>`.__T__getSigRatio:topGO`</w>
-      <w>`.__T__getSpline:Rgraphviz`</w>
-      <w>`.__T__getTable:rtracklayer`</w>
-      <w>`.__T__getTranscriptSeqs:VariantAnnotation`</w>
-      <w>`.__T__getTrellis:ShortRead`</w>
-      <w>`.__T__getUnmeth:minfi`</w>
-      <w>`.__T__getValues:raster`</w>
-      <w>`.__T__getValuesBlock:raster`</w>
-      <w>`.__T__getValuesFocal:raster`</w>
-      <w>`.__T__getX:Rgraphviz`</w>
-      <w>`.__T__getXLab:biovizBase`</w>
-      <w>`.__T__getXScale:biovizBase`</w>
-      <w>`.__T__getY:Rgraphviz`</w>
-      <w>`.__T__getYLab:biovizBase`</w>
-      <w>`.__T__get_adaptation_info:rstan`</w>
-      <w>`.__T__get_cppcode:rstan`</w>
-      <w>`.__T__get_cppo_mode:rstan`</w>
-      <w>`.__T__get_cxxflags:rstan`</w>
-      <w>`.__T__get_elapsed_time:rstan`</w>
-      <w>`.__T__get_inits:rstan`</w>
-      <w>`.__T__get_logposterior:rstan`</w>
-      <w>`.__T__get_num_upars:rstan`</w>
-      <w>`.__T__get_posterior_mean:rstan`</w>
-      <w>`.__T__get_sampler_params:rstan`</w>
-      <w>`.__T__get_seed:rstan`</w>
-      <w>`.__T__get_seeds:rstan`</w>
-      <w>`.__T__get_stancode:rstan`</w>
-      <w>`.__T__get_stanmodel:rstan`</w>
-      <w>`.__T__goDag:GOstats`</w>
-      <w>`.__T__goSlim:GSEABase`</w>
-      <w>`.__T__grad_log_prob:rstan`</w>
-      <w>`.__T__granges:GenomicRanges`</w>
-      <w>`.__T__graph:topGO`</w>
-      <w>`.__T__graph&lt;-:topGO`</w>
-      <w>`.__T__graphData:Rgraphviz`</w>
-      <w>`.__T__graphData&lt;-:Rgraphviz`</w>
-      <w>`.__T__graphDataDefaults:Rgraphviz`</w>
-      <w>`.__T__graphDataDefaults&lt;-:Rgraphviz`</w>
-      <w>`.__T__graphIntersect:graph`</w>
-      <w>`.__T__graphUnion:graph`</w>
-      <w>`.__T__grep:BiocGenerics`</w>
-      <w>`.__T__grepl:BiocGenerics`</w>
-      <w>`.__T__grglist:GenomicRanges`</w>
-      <w>`.__T__gridDistance:raster`</w>
-      <w>`.__T__gridded:sp`</w>
-      <w>`.__T__gridded&lt;-:sp`</w>
-      <w>`.__T__grobify:grImport`</w>
-      <w>`.__T__group:Gviz`</w>
-      <w>`.__T__group:flexmix`</w>
-      <w>`.__T__group&lt;-:Gviz`</w>
-      <w>`.__T__groupReport:PWMEnrich`</w>
-      <w>`.__T__grouplengths:IRanges`</w>
-      <w>`.__T__grouprank:IRanges`</w>
-      <w>`.__T__groups_factor:IHW`</w>
-      <w>`.__T__gsub:base`</w>
-      <w>`.__T__gsva:GSVA`</w>
-      <w>`.__T__hardFilters:VariantAnnotation`</w>
-      <w>`.__T__hardFilters&lt;-:VariantAnnotation`</w>
-      <w>`.__T__has:modeltools`</w>
-      <w>`.__T__hasAllFlinks:Biostrings`</w>
-      <w>`.__T__hasMultiProbes:AnnotationDbi`</w>
-      <w>`.__T__hasOnlyBaseLetters:Biostrings`</w>
-      <w>`.__T__hasProteinData:ensembldb`</w>
-      <w>`.__T__hasSingleProbes:AnnotationDbi`</w>
-      <w>`.__T__hcell2xy:hexbin`</w>
-      <w>`.__T__head:utils`</w>
-      <w>`.__T__header:VariantAnnotation`</w>
-      <w>`.__T__header&lt;-:VariantAnnotation`</w>
-      <w>`.__T__headerTabix:Rsamtools`</w>
-      <w>`.__T__high2low:IRanges`</w>
-      <w>`.__T__hist:graphics`</w>
-      <w>`.__T__homoACC:annotate`</w>
-      <w>`.__T__homoHGID:annotate`</w>
-      <w>`.__T__homoLL:annotate`</w>
-      <w>`.__T__homoOrg:annotate`</w>
-      <w>`.__T__homoPS:annotate`</w>
-      <w>`.__T__homoType:annotate`</w>
-      <w>`.__T__homoURL:annotate`</w>
-      <w>`.__T__hour&lt;-:lubridate`</w>
-      <w>`.__T__how:kernlab`</w>
-      <w>`.__T__hsmooth:hexbin`</w>
-      <w>`.__T__htmlReport:Category`</w>
-      <w>`.__T__hubCache:AnnotationHub`</w>
-      <w>`.__T__hubDate:AnnotationHub`</w>
-      <w>`.__T__hubUrl:AnnotationHub`</w>
-      <w>`.__T__hybridizations:Biobase`</w>
-      <w>`.__T__hyperGTest:Category`</w>
-      <w>`.__T__hyperg:Category`</w>
-      <w>`.__T__id:ShortRead`</w>
-      <w>`.__T__idType:VariantAnnotation`</w>
-      <w>`.__T__idType&lt;-:VariantAnnotation`</w>
-      <w>`.__T__idconv:systemPipeR`</w>
-      <w>`.__T__identifier:Gviz`</w>
-      <w>`.__T__identifier&lt;-:Gviz`</w>
-      <w>`.__T__identify:graphics`</w>
-      <w>`.__T__ids:GSEABase`</w>
-      <w>`.__T__idxstatsBam:Rsamtools`</w>
-      <w>`.__T__ifelse2:IRanges`</w>
-      <w>`.__T__ignore.strand:ShortRead`</w>
-      <w>`.__T__image:graphics`</w>
-      <w>`.__T__imageMap:Gviz`</w>
-      <w>`.__T__imageMap:geneplotter`</w>
-      <w>`.__T__import.2bit:rtracklayer`</w>
-      <w>`.__T__import.bed15:rtracklayer`</w>
-      <w>`.__T__import.bed:rtracklayer`</w>
-      <w>`.__T__import.bedGraph:rtracklayer`</w>
-      <w>`.__T__import.bw:rtracklayer`</w>
-      <w>`.__T__import.chain:rtracklayer`</w>
-      <w>`.__T__import.gff1:rtracklayer`</w>
-      <w>`.__T__import.gff2:rtracklayer`</w>
-      <w>`.__T__import.gff3:rtracklayer`</w>
-      <w>`.__T__import.gff:rtracklayer`</w>
-      <w>`.__T__import.ucsc:rtracklayer`</w>
-      <w>`.__T__import.wig:rtracklayer`</w>
-      <w>`.__T__import:rtracklayer`</w>
-      <w>`.__T__importPublicData:CAGEr`</w>
-      <w>`.__T__improvedCV2:scran`</w>
-      <w>`.__T__inEdges:graph`</w>
-      <w>`.__T__inchol:kernlab`</w>
-      <w>`.__T__incidence:GSEABase`</w>
-      <w>`.__T__indel:Biostrings`</w>
-      <w>`.__T__index:Rsamtools`</w>
-      <w>`.__T__index&lt;-:Rsamtools`</w>
-      <w>`.__T__indexBam:Rsamtools`</w>
-      <w>`.__T__indexBcf:Rsamtools`</w>
-      <w>`.__T__indexFa:Rsamtools`</w>
-      <w>`.__T__indexProbes:affy`</w>
-      <w>`.__T__indexVcf:VariantAnnotation`</w>
-      <w>`.__T__infile1:systemPipeR`</w>
-      <w>`.__T__infile2:systemPipeR`</w>
-      <w>`.__T__info:VariantAnnotation`</w>
-      <w>`.__T__info:modeltools`</w>
-      <w>`.__T__info&lt;-:VariantAnnotation`</w>
-      <w>`.__T__initfun:Biobase`</w>
-      <w>`.__T__initialize:methods`</w>
-      <w>`.__T__injectHardMask:Biostrings`</w>
-      <w>`.__T__injectSNPs:BSgenome`</w>
-      <w>`.__T__inlearn:kernlab`</w>
-      <w>`.__T__inputFiles:CAGEr`</w>
-      <w>`.__T__inputFilesType:CAGEr`</w>
-      <w>`.__T__insertion:Biostrings`</w>
-      <w>`.__T__intensities.IB:methylumi`</w>
-      <w>`.__T__intensities.M:methylumi`</w>
-      <w>`.__T__intensities.OOB.allelic:methylumi`</w>
-      <w>`.__T__intensities.OOB:methylumi`</w>
-      <w>`.__T__intensities.U:methylumi`</w>
-      <w>`.__T__intensitiesByChannel:methylumi`</w>
-      <w>`.__T__intensity:ProtGenerics`</w>
-      <w>`.__T__intensity:affy`</w>
-      <w>`.__T__intensity&lt;-:affy`</w>
-      <w>`.__T__intergenic:VariantAnnotation`</w>
-      <w>`.__T__intergenic&lt;-:VariantAnnotation`</w>
-      <w>`.__T__interpolate:raster`</w>
-      <w>`.__T__intersect:BiocGenerics`</w>
-      <w>`.__T__intersect:base`</w>
-      <w>`.__T__intersection2:graph`</w>
-      <w>`.__T__intersection:graph`</w>
-      <w>`.__T__intersectlist:systemPipeR`</w>
-      <w>`.__T__intersectmatrix:systemPipeR`</w>
-      <w>`.__T__interval_complement:intervals`</w>
-      <w>`.__T__interval_difference:intervals`</w>
-      <w>`.__T__interval_included:intervals`</w>
-      <w>`.__T__interval_intersection:intervals`</w>
-      <w>`.__T__interval_overlap:intervals`</w>
-      <w>`.__T__interval_union:intervals`</w>
-      <w>`.__T__intronsByTranscript:GenomicFeatures`</w>
-      <w>`.__T__inverse:dimRed`</w>
-      <w>`.__T__invertStrand:BiocGenerics`</w>
-      <w>`.__T__ions:ProtGenerics`</w>
-      <w>`.__T__ipop:kernlab`</w>
-      <w>`.__T__is.factor:base`</w>
-      <w>`.__T__is.finite:base`</w>
-      <w>`.__T__is.infinite:base`</w>
-      <w>`.__T__is.na:base`</w>
-      <w>`.__T__is.nan:base`</w>
-      <w>`.__T__is.projected:sp`</w>
-      <w>`.__T__is.unsorted:BiocGenerics`</w>
-      <w>`.__T__isActiveSeq:GenomicFeatures`</w>
-      <w>`.__T__isActiveSeq&lt;-:GenomicFeatures`</w>
-      <w>`.__T__isAdjacent:graph`</w>
-      <w>`.__T__isCentroided:ProtGenerics`</w>
-      <w>`.__T__isCircular:GenomeInfoDb`</w>
-      <w>`.__T__isCircular&lt;-:GenomeInfoDb`</w>
-      <w>`.__T__isClassic:rrcov`</w>
-      <w>`.__T__isCompatibleWithSkippedExons:GenomicAlignments`</w>
-      <w>`.__T__isCompatibleWithSplicing:GenomicAlignments`</w>
-      <w>`.__T__isConnected:graph`</w>
-      <w>`.__T__isConstant:S4Vectors`</w>
-      <w>`.__T__isCurrent:Biobase`</w>
-      <w>`.__T__isDaily:timeDate`</w>
-      <w>`.__T__isDeletion:VariantAnnotation`</w>
-      <w>`.__T__isDelins:VariantAnnotation`</w>
-      <w>`.__T__isDiagonal:Matrix`</w>
-      <w>`.__T__isDirected:graph`</w>
-      <w>`.__T__isDisjoint:IRanges`</w>
-      <w>`.__T__isEmpty:S4Vectors`</w>
-      <w>`.__T__isIncomplete:base`</w>
-      <w>`.__T__isIndel:VariantAnnotation`</w>
-      <w>`.__T__isInsertion:VariantAnnotation`</w>
-      <w>`.__T__isLinear:DelayedArray`</w>
-      <w>`.__T__isLonLat:raster`</w>
-      <w>`.__T__isMatchingEndingAt:Biostrings`</w>
-      <w>`.__T__isMatchingStartingAt:Biostrings`</w>
-      <w>`.__T__isMonthly:timeDate`</w>
-      <w>`.__T__isNA:AnnotationDbi`</w>
-      <w>`.__T__isNormal:IRanges`</w>
-      <w>`.__T__isOpen:base`</w>
-      <w>`.__T__isProperPair:GenomicAlignments`</w>
-      <w>`.__T__isQuarterly:timeDate`</w>
-      <w>`.__T__isRegular:timeDate`</w>
-      <w>`.__T__isSNV:VariantAnnotation`</w>
-      <w>`.__T__isSQLKeyword:DBI`</w>
-      <w>`.__T__isSingular:rrcov`</w>
-      <w>`.__T__isSorted:S4Vectors`</w>
-      <w>`.__T__isSpike:SingleCellExperiment`</w>
-      <w>`.__T__isSpike&lt;-:SingleCellExperiment`</w>
-      <w>`.__T__isStrictlySorted:S4Vectors`</w>
-      <w>`.__T__isSubstitution:VariantAnnotation`</w>
-      <w>`.__T__isSymmetric:base`</w>
-      <w>`.__T__isTransition:VariantAnnotation`</w>
-      <w>`.__T__isTriangular:Matrix`</w>
-      <w>`.__T__isVersioned:Biobase`</w>
-      <w>`.__T__join:graph`</w>
-      <w>`.__T__joinFun:topGO`</w>
-      <w>`.__T__journal:annotate`</w>
-      <w>`.__T__julian:base`</w>
-      <w>`.__T__junctions:GenomicAlignments`</w>
-      <w>`.__T__kcall:kernlab`</w>
-      <w>`.__T__kcca:kernlab`</w>
-      <w>`.__T__kcor:kernlab`</w>
-      <w>`.__T__kernelFast:kernlab`</w>
-      <w>`.__T__kernelMatrix:kernlab`</w>
-      <w>`.__T__kernelMult:kernlab`</w>
-      <w>`.__T__kernelPol:kernlab`</w>
-      <w>`.__T__kernelf:kernlab`</w>
-      <w>`.__T__keyname:AnnotationDbi`</w>
-      <w>`.__T__keys:AnnotationDbi`</w>
-      <w>`.__T__keys&lt;-:AnnotationDbi`</w>
-      <w>`.__T__keytypes:AnnotationDbi`</w>
-      <w>`.__T__kfa:kernlab`</w>
-      <w>`.__T__kha:kernlab`</w>
-      <w>`.__T__kkmeans:kernlab`</w>
-      <w>`.__T__kmmd:kernlab`</w>
-      <w>`.__T__kpar:kernlab`</w>
-      <w>`.__T__kpca:kernlab`</w>
-      <w>`.__T__kqr:kernlab`</w>
-      <w>`.__T__kronecker:base`</w>
-      <w>`.__T__ksvm:kernlab`</w>
-      <w>`.__T__label:maptools`</w>
-      <w>`.__T__labelColor:Rgraphviz`</w>
-      <w>`.__T__labelFontsize:Rgraphviz`</w>
-      <w>`.__T__labelJust:Rgraphviz`</w>
-      <w>`.__T__labelLoc:Rgraphviz`</w>
-      <w>`.__T__labelText:Rgraphviz`</w>
-      <w>`.__T__labelWidth:Rgraphviz`</w>
-      <w>`.__T__labels:base`</w>
-      <w>`.__T__laidout:Rgraphviz`</w>
-      <w>`.__T__laneNames:ShortRead`</w>
-      <w>`.__T__lapply:BiocGenerics`</w>
-      <w>`.__T__last:GenomicAlignments`</w>
-      <w>`.__T__layerize:raster`</w>
-      <w>`.__T__layoutType:Rgraphviz`</w>
-      <w>`.__T__lcprefix:Biostrings`</w>
-      <w>`.__T__lcsubstr:Biostrings`</w>
-      <w>`.__T__lcsuffix:Biostrings`</w>
-      <w>`.__T__leaves:graph`</w>
-      <w>`.__T__left:ShortRead`</w>
-      <w>`.__T__length:base`</w>
-      <w>`.__T__length&lt;-:base`</w>
-      <w>`.__T__lengthOf:ensembldb`</w>
-      <w>`.__T__lengths:BiocGenerics`</w>
-      <w>`.__T__letter:Biostrings`</w>
-      <w>`.__T__letterFrequency:Biostrings`</w>
-      <w>`.__T__letterFrequencyInSlidingView:Biostrings`</w>
-      <w>`.__T__lev:kernlab`</w>
-      <w>`.__T__level2nodes:Category`</w>
-      <w>`.__T__levels:base`</w>
-      <w>`.__T__levels&lt;-:base`</w>
-      <w>`.__T__lgamma:base`</w>
-      <w>`.__T__lgeneIds:Category`</w>
-      <w>`.__T__librarySizes:CAGEr`</w>
-      <w>`.__T__liftOver:rtracklayer`</w>
-      <w>`.__T__linearMTest:Category`</w>
-      <w>`.__T__lines:graphics`</w>
-      <w>`.__T__links:AnnotationDbi`</w>
-      <w>`.__T__listColumns:ensembldb`</w>
-      <w>`.__T__listGenebiotypes:ensembldb`</w>
-      <w>`.__T__listResources:AnnotationHub`</w>
-      <w>`.__T__listTables:ensembldb`</w>
-      <w>`.__T__listTxbiotypes:ensembldb`</w>
-      <w>`.__T__listUniprotDbs:ensembldb`</w>
-      <w>`.__T__listUniprotMappingTypes:ensembldb`</w>
-      <w>`.__T__loadMethod:methods`</w>
-      <w>`.__T__loadResources:AnnotationHub`</w>
-      <w>`.__T__localFun:raster`</w>
-      <w>`.__T__locateVariants:VariantAnnotation`</w>
-      <w>`.__T__locked:Biobase`</w>
-      <w>`.__T__log10:base`</w>
-      <w>`.__T__log2:base`</w>
-      <w>`.__T__log:base`</w>
-      <w>`.__T__logLik:stats`</w>
-      <w>`.__T__log_prob:rstan`</w>
-      <w>`.__T__logcounts:SingleCellExperiment`</w>
-      <w>`.__T__logcounts&lt;-:SingleCellExperiment`</w>
-      <w>`.__T__logicOp:AnnotationFilter`</w>
-      <w>`.__T__longDescription:GSEABase`</w>
-      <w>`.__T__longDescription&lt;-:GSEABase`</w>
-      <w>`.__T__longFormat:MultiAssayExperiment`</w>
-      <w>`.__T__loo:loo`</w>
-      <w>`.__T__low2high:IRanges`</w>
-      <w>`.__T__lower.tri:base`</w>
-      <w>`.__T__ls:base`</w>
-      <w>`.__T__lssvm:kernlab`</w>
-      <w>`.__T__lu:Matrix`</w>
-      <w>`.__T__m_groups:IHW`</w>
-      <w>`.__T__maA:marray`</w>
-      <w>`.__T__maA&lt;-:marray`</w>
-      <w>`.__T__maControls:marray`</w>
-      <w>`.__T__maControls&lt;-:marray`</w>
-      <w>`.__T__maGb:marray`</w>
-      <w>`.__T__maGb&lt;-:marray`</w>
-      <w>`.__T__maGf:marray`</w>
-      <w>`.__T__maGf&lt;-:marray`</w>
-      <w>`.__T__maGnames:marray`</w>
-      <w>`.__T__maGnames&lt;-:marray`</w>
-      <w>`.__T__maGridCol:marray`</w>
-      <w>`.__T__maGridRow:marray`</w>
-      <w>`.__T__maInfo:marray`</w>
-      <w>`.__T__maInfo&lt;-:marray`</w>
-      <w>`.__T__maLG:marray`</w>
-      <w>`.__T__maLR:marray`</w>
-      <w>`.__T__maLabels:marray`</w>
-      <w>`.__T__maLabels&lt;-:marray`</w>
-      <w>`.__T__maLayout:marray`</w>
-      <w>`.__T__maLayout&lt;-:marray`</w>
-      <w>`.__T__maM:marray`</w>
-      <w>`.__T__maM&lt;-:marray`</w>
-      <w>`.__T__maMloc:marray`</w>
-      <w>`.__T__maMloc&lt;-:marray`</w>
-      <w>`.__T__maMscale:marray`</w>
-      <w>`.__T__maMscale&lt;-:marray`</w>
-      <w>`.__T__maNgc:marray`</w>
-      <w>`.__T__maNgc&lt;-:marray`</w>
-      <w>`.__T__maNgr:marray`</w>
-      <w>`.__T__maNgr&lt;-:marray`</w>
-      <w>`.__T__maNormCall:marray`</w>
-      <w>`.__T__maNotes:marray`</w>
-      <w>`.__T__maNotes&lt;-:marray`</w>
-      <w>`.__T__maNsamples:marray`</w>
-      <w>`.__T__maNsc:marray`</w>
-      <w>`.__T__maNsc&lt;-:marray`</w>
-      <w>`.__T__maNspots:marray`</w>
-      <w>`.__T__maNspots&lt;-:marray`</w>
-      <w>`.__T__maNsr:marray`</w>
-      <w>`.__T__maNsr&lt;-:marray`</w>
-      <w>`.__T__maPlate:marray`</w>
-      <w>`.__T__maPlate&lt;-:marray`</w>
-      <w>`.__T__maPrintTip:marray`</w>
-      <w>`.__T__maRb:marray`</w>
-      <w>`.__T__maRb&lt;-:marray`</w>
-      <w>`.__T__maRf:marray`</w>
-      <w>`.__T__maRf&lt;-:marray`</w>
-      <w>`.__T__maSpotCol:marray`</w>
-      <w>`.__T__maSpotRow:marray`</w>
-      <w>`.__T__maSub:marray`</w>
-      <w>`.__T__maTargets:marray`</w>
-      <w>`.__T__maTargets&lt;-:marray`</w>
-      <w>`.__T__maW:marray`</w>
-      <w>`.__T__maW&lt;-:marray`</w>
-      <w>`.__T__mad:BiocGenerics`</w>
-      <w>`.__T__mainPage:annotate`</w>
-      <w>`.__T__make.db.names:DBI`</w>
-      <w>`.__T__makeAnnDbPkg:AnnotationForge`</w>
-      <w>`.__T__makeDataPackage:Biobase`</w>
-      <w>`.__T__makeValidParams:Category`</w>
-      <w>`.__T__mapFromAlignments:GenomicAlignments`</w>
-      <w>`.__T__mapFromTranscripts:GenomicFeatures`</w>
-      <w>`.__T__mapIdentifiers:GSEABase`</w>
-      <w>`.__T__mapIds:AnnotationDbi`</w>
-      <w>`.__T__mapIdsToRanges:GenomicFeatures`</w>
-      <w>`.__T__mapOrder:IRanges`</w>
-      <w>`.__T__mapRangesToIds:GenomicFeatures`</w>
-      <w>`.__T__mapToAlignments:GenomicAlignments`</w>
-      <w>`.__T__mapToGenome:minfi`</w>
-      <w>`.__T__mapToTranscripts:GenomicFeatures`</w>
-      <w>`.__T__mappedLkeys:AnnotationDbi`</w>
-      <w>`.__T__mappedRkeys:AnnotationDbi`</w>
-      <w>`.__T__mappedkeys:AnnotationDbi`</w>
-      <w>`.__T__mapply:BiocGenerics`</w>
-      <w>`.__T__mas5calls:affy`</w>
-      <w>`.__T__mask:raster`</w>
-      <w>`.__T__maskGaps:Biostrings`</w>
-      <w>`.__T__maskMotif:Biostrings`</w>
-      <w>`.__T__maskeddim:Biostrings`</w>
-      <w>`.__T__maskedncol:Biostrings`</w>
-      <w>`.__T__maskednrow:Biostrings`</w>
-      <w>`.__T__maskedratio:IRanges`</w>
-      <w>`.__T__maskedwidth:IRanges`</w>
-      <w>`.__T__masknames:BSgenome`</w>
-      <w>`.__T__masks:Biostrings`</w>
-      <w>`.__T__masks&lt;-:Biostrings`</w>
-      <w>`.__T__mass:ProtGenerics`</w>
-      <w>`.__T__match:BiocGenerics`</w>
-      <w>`.__T__match:base`</w>
-      <w>`.__T__matchDistribution:CNEr`</w>
-      <w>`.__T__matchLRPatterns:Biostrings`</w>
-      <w>`.__T__matchPDict:Biostrings`</w>
-      <w>`.__T__matchPWM:Biostrings`</w>
-      <w>`.__T__matchPattern:Biostrings`</w>
-      <w>`.__T__matchProbePair:Biostrings`</w>
-      <w>`.__T__matrixClass:DelayedArray`</w>
-      <w>`.__T__max:base`</w>
-      <w>`.__T__maxGap:biovizBase`</w>
-      <w>`.__T__maxScore:Biostrings`</w>
-      <w>`.__T__maxValue:raster`</w>
-      <w>`.__T__maxWeights:Biostrings`</w>
-      <w>`.__T__maximize_correlation:dimRed`</w>
-      <w>`.__T__maxresiduals:kernlab`</w>
-      <w>`.__T__mcols:S4Vectors`</w>
-      <w>`.__T__mcols&lt;-:S4Vectors`</w>
-      <w>`.__T__mean:base`</w>
-      <w>`.__T__meanSdPlot:vsn`</w>
-      <w>`.__T__mean_R_NX:dimRed`</w>
-      <w>`.__T__median:stats`</w>
-      <w>`.__T__members:IRanges`</w>
-      <w>`.__T__members:topGO`</w>
-      <w>`.__T__members&lt;-:topGO`</w>
-      <w>`.__T__membersExpr:topGO`</w>
-      <w>`.__T__membersScore:topGO`</w>
-      <w>`.__T__mendoapply:S4Vectors`</w>
-      <w>`.__T__merge:base`</w>
-      <w>`.__T__mergeBam:Rsamtools`</w>
-      <w>`.__T__mergeCAGEsets:CAGEr`</w>
-      <w>`.__T__mergeReplicates:MultiAssayExperiment`</w>
-      <w>`.__T__mergeSamples:CAGEr`</w>
-      <w>`.__T__meta:VariantAnnotation`</w>
-      <w>`.__T__meta&lt;-:VariantAnnotation`</w>
-      <w>`.__T__metadata:S4Vectors`</w>
-      <w>`.__T__metadata&lt;-:S4Vectors`</w>
-      <w>`.__T__methylated.N:methylumi`</w>
-      <w>`.__T__methylated.N&lt;-:methylumi`</w>
-      <w>`.__T__methylated:methylumi`</w>
-      <w>`.__T__methylated&lt;-:methylumi`</w>
-      <w>`.__T__metrics:beadarray`</w>
-      <w>`.__T__mgEdgeData:graph`</w>
-      <w>`.__T__mgEdgeData&lt;-:graph`</w>
-      <w>`.__T__mgEdgeDataDefaults:graph`</w>
-      <w>`.__T__mgEdgeDataDefaults&lt;-:graph`</w>
-      <w>`.__T__mget:BiocGenerics`</w>
-      <w>`.__T__microRNAs:GenomicFeatures`</w>
-      <w>`.__T__mid:IRanges`</w>
-      <w>`.__T__min:base`</w>
-      <w>`.__T__minScore:Biostrings`</w>
-      <w>`.__T__minValue:raster`</w>
-      <w>`.__T__minWeights:Biostrings`</w>
-      <w>`.__T__minute&lt;-:lubridate`</w>
-      <w>`.__T__mismatch:Biostrings`</w>
-      <w>`.__T__mismatchSummary:Biostrings`</w>
-      <w>`.__T__mismatchTable:Biostrings`</w>
-      <w>`.__T__mlike:kernlab`</w>
-      <w>`.__T__mm:affy`</w>
-      <w>`.__T__mm&lt;-:affy`</w>
-      <w>`.__T__mmdstats:kernlab`</w>
-      <w>`.__T__mmindex:affy`</w>
-      <w>`.__T__modal:raster`</w>
-      <w>`.__T__model.guess:SparseM`</w>
-      <w>`.__T__model.matrix:stats`</w>
-      <w>`.__T__model.response:stats`</w>
-      <w>`.__T__model.xexact:SparseM`</w>
-      <w>`.__T__modifications:ProtGenerics`</w>
-      <w>`.__T__modules:systemPipeR`</w>
-      <w>`.__T__mold:biovizBase`</w>
-      <w>`.__T__month&lt;-:lubridate`</w>
-      <w>`.__T__months:base`</w>
-      <w>`.__T__mosaic:raster`</w>
-      <w>`.__T__motifRankingForGroup:PWMEnrich`</w>
-      <w>`.__T__motifRankingForSequence:PWMEnrich`</w>
-      <w>`.__T__mseqnames:BSgenome`</w>
-      <w>`.__T__mstack:IRanges`</w>
-      <w>`.__T__mtp2ebmtp:multtest`</w>
-      <w>`.__T__mutate:scater`</w>
-      <w>`.__T__mz:ProtGenerics`</w>
-      <w>`.__T__mz&lt;-:ProtGenerics`</w>
-      <w>`.__T__nChrom:annotate`</w>
-      <w>`.__T__nLnode:S4Vectors`</w>
-      <w>`.__T__nObservations:beadarray`</w>
-      <w>`.__T__nObservations&lt;-:beadarray`</w>
-      <w>`.__T__nRnode:S4Vectors`</w>
-      <w>`.__T__nSV:kernlab`</w>
-      <w>`.__T__na.exclude:stats`</w>
-      <w>`.__T__na.fail:stats`</w>
-      <w>`.__T__na.omit:stats`</w>
-      <w>`.__T__na.pass:stats`</w>
-      <w>`.__T__name:Rgraphviz`</w>
-      <w>`.__T__name:ShortRead`</w>
-      <w>`.__T__names:base`</w>
-      <w>`.__T__names&lt;-:base`</w>
-      <w>`.__T__nanes:wateRmelon`</w>
-      <w>`.__T__nanet:wateRmelon`</w>
-      <w>`.__T__narrow:IRanges`</w>
-      <w>`.__T__nasen:wateRmelon`</w>
-      <w>`.__T__naten:wateRmelon`</w>
-      <w>`.__T__nbins:IHW`</w>
-      <w>`.__T__ncell:raster`</w>
-      <w>`.__T__nchar:base`</w>
-      <w>`.__T__ncol:base`</w>
-      <w>`.__T__ncol&lt;-:raster`</w>
-      <w>`.__T__ndims:dimRed`</w>
-      <w>`.__T__nearest:IRanges`</w>
-      <w>`.__T__nedit:Biostrings`</w>
-      <w>`.__T__neditEndingAt:Biostrings`</w>
-      <w>`.__T__neditStartingAt:Biostrings`</w>
-      <w>`.__T__needwunsQS:Biostrings`</w>
-      <w>`.__T__negctls.stderr:methylumi`</w>
-      <w>`.__T__negctls:methylumi`</w>
-      <w>`.__T__negnorm:methylumi`</w>
-      <w>`.__T__nfolds:IHW`</w>
-      <w>`.__T__nhit:AnnotationDbi`</w>
-      <w>`.__T__nindel:Biostrings`</w>
-      <w>`.__T__nir_list:IRanges`</w>
-      <w>`.__T__njunc:GenomicAlignments`</w>
-      <w>`.__T__nlayers:raster`</w>
-      <w>`.__T__nmatch:Biostrings`</w>
-      <w>`.__T__nmismatch:Biostrings`</w>
-      <w>`.__T__nnode:S4Vectors`</w>
-      <w>`.__T__nnodes:Biostrings`</w>
-      <w>`.__T__nnzero:Matrix`</w>
-      <w>`.__T__nobj:IRanges`</w>
-      <w>`.__T__nobs:stats`</w>
-      <w>`.__T__nodeData:graph`</w>
-      <w>`.__T__nodeData&lt;-:graph`</w>
-      <w>`.__T__nodeDataDefaults:graph`</w>
-      <w>`.__T__nodeDataDefaults&lt;-:graph`</w>
-      <w>`.__T__nodes:graph`</w>
-      <w>`.__T__nodes&lt;-:graph`</w>
-      <w>`.__T__norm:base`</w>
-      <w>`.__T__normControls:Biobase`</w>
-      <w>`.__T__normOffsets:csaw`</w>
-      <w>`.__T__norm_exprs:scater`</w>
-      <w>`.__T__norm_exprs&lt;-:scater`</w>
-      <w>`.__T__normalizationFactor:DSS`</w>
-      <w>`.__T__normalizationFactor&lt;-:DSS`</w>
-      <w>`.__T__normalizationFactors:DESeq2`</w>
-      <w>`.__T__normalizationFactors&lt;-:DESeq2`</w>
-      <w>`.__T__normalize.methods:affy`</w>
-      <w>`.__T__normalize:BiocGenerics`</w>
-      <w>`.__T__normalizeSingleBracketReplacementValue:S4Vectors`</w>
-      <w>`.__T__normalizeTagCount:CAGEr`</w>
-      <w>`.__T__normcounts:SingleCellExperiment`</w>
-      <w>`.__T__normcounts&lt;-:SingleCellExperiment`</w>
-      <w>`.__T__normctls:methylumi`</w>
-      <w>`.__T__not:AnnotationFilter`</w>
-      <w>`.__T__notes:Biobase`</w>
-      <w>`.__T__notes&lt;-:Biobase`</w>
-      <w>`.__T__nrow:base`</w>
-      <w>`.__T__nrow&lt;-:raster`</w>
-      <w>`.__T__nrun:S4Vectors`</w>
-      <w>`.__T__nsFilter:genefilter`</w>
-      <w>`.__T__nucleotideFrequencyAt:Biostrings`</w>
-      <w>`.__T__numAllMembers:topGO`</w>
-      <w>`.__T__numBeads:beadarray`</w>
-      <w>`.__T__numEdges:graph`</w>
-      <w>`.__T__numGenes:topGO`</w>
-      <w>`.__T__numMembers:topGO`</w>
-      <w>`.__T__numNodes:graph`</w>
-      <w>`.__T__numSigAll:topGO`</w>
-      <w>`.__T__numSigGenes:topGO`</w>
-      <w>`.__T__numSigMembers:topGO`</w>
-      <w>`.__T__numSplines:Rgraphviz`</w>
-      <w>`.__T__nvar:kernlab`</w>
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-      <w>`.__T__overlay:raster`</w>
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-      <w>`.__T__parLapplyLB:BiocGenerics`</w>
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-      <w>`.__T__parSapplyLB:BiocGenerics`</w>
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-      <w>`.__T__peptides:ProtGenerics`</w>
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-      <w>`.__T__persp:graphics`</w>
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-      <w>`.__T__pintersect:IRanges`</w>
-      <w>`.__T__pivots:kernlab`</w>
-      <w>`.__T__plogis:stats`</w>
-      <w>`.__T__plot:graphics`</w>
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-      <w>`.__T__plotAnnoPie:ChIPseeker`</w>
-      <w>`.__T__plotCorrelation:CAGEr`</w>
-      <w>`.__T__plotDispEsts:BiocGenerics`</w>
-      <w>`.__T__plotDistToTSS:ChIPseeker`</w>
-      <w>`.__T__plotExpressionProfiles:CAGEr`</w>
-      <w>`.__T__plotInterquantileWidth:CAGEr`</w>
-      <w>`.__T__plotMA:BiocGenerics`</w>
-      <w>`.__T__plotNAs:methylumi`</w>
-      <w>`.__T__plotPCA:BiocGenerics`</w>
-      <w>`.__T__plotRGB:raster`</w>
-      <w>`.__T__plotReverseCumulatives:CAGEr`</w>
-      <w>`.__T__plotSampleIntensities:methylumi`</w>
-      <w>`.__T__plotTopMotifsGroup:PWMEnrich`</w>
-      <w>`.__T__plotTopMotifsSequence:PWMEnrich`</w>
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-      <w>`.__T__pmapToAlignments:GenomicAlignments`</w>
-      <w>`.__T__pmapToTranscripts:GenomicFeatures`</w>
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-      <w>`.__T__ppois:stats`</w>
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-      <w>`.__T__readGAlignments:GenomicAlignments`</w>
-      <w>`.__T__readGAlignmentsList:GenomicAlignments`</w>
-      <w>`.__T__readGappedReads:GenomicAlignments`</w>
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-      <w>`.__T__readHTMLTable:XML`</w>
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-      <w>`.__T__readKeyValueDB:XML`</w>
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-      <w>`.__T__readQual:ShortRead`</w>
-      <w>`.__T__readSolrDoc:XML`</w>
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-      <w>`.__T__removeAttributes:XML`</w>
-      <w>`.__T__removeEdge:graph`</w>
-      <w>`.__T__removeEdgesByWeight:graph`</w>
-      <w>`.__T__removeNode:graph`</w>
-      <w>`.__T__removeXMLNamespaces:XML`</w>
-      <w>`.__T__rename:S4Vectors`</w>
-      <w>`.__T__rename:scater`</w>
-      <w>`.__T__renderGraph:Rgraphviz`</w>
-      <w>`.__T__renew:ShortRead`</w>
-      <w>`.__T__renewable:ShortRead`</w>
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-      <w>`.__T__rep:base`</w>
-      <w>`.__T__replaceAt:Biostrings`</w>
-      <w>`.__T__replaceLetterAt:Biostrings`</w>
-      <w>`.__T__replaceROWS:S4Vectors`</w>
-      <w>`.__T__report:ShortRead`</w>
-      <w>`.__T__report_html:ShortRead`</w>
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-      <w>`.__T__reset:RCurl`</w>
-      <w>`.__T__resid:stats`</w>
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-      <w>`.__T__resize:IRanges`</w>
-      <w>`.__T__restimate:rrcov`</w>
-      <w>`.__T__restore:ShortRead`</w>
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-      <w>`.__T__results:systemPipeR`</w>
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-      <w>`.__T__returnFilterColumns&lt;-:ensembldb`</w>
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-      <w>`.__T__reverseComplement:Biostrings`</w>
-      <w>`.__T__reversed:rtracklayer`</w>
-      <w>`.__T__revmap:AnnotationDbi`</w>
-      <w>`.__T__reweightPred:MatrixModels`</w>
-      <w>`.__T__rflexmix:flexmix`</w>
-      <w>`.__T__rglist:IRanges`</w>
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-      <w>`.__T__right:ShortRead`</w>
-      <w>`.__T__rname:GenomicAlignments`</w>
-      <w>`.__T__rname&lt;-:GenomicAlignments`</w>
-      <w>`.__T__rotate:raster`</w>
-      <w>`.__T__rotated:kernlab`</w>
-      <w>`.__T__round:base`</w>
-      <w>`.__T__rowColFromCell:raster`</w>
-      <w>`.__T__rowData:SummarizedExperiment`</w>
-      <w>`.__T__rowData&lt;-:SummarizedExperiment`</w>
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-      <w>`.__T__rowFromY:raster`</w>
-      <w>`.__T__rowFtests:genefilter`</w>
-      <w>`.__T__rowMaxs:DelayedArray`</w>
-      <w>`.__T__rowMeans:BiocGenerics`</w>
-      <w>`.__T__rowMeans:base`</w>
-      <w>`.__T__rowMedians:Biobase`</w>
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-      <w>`.__T__rowQ:Biobase`</w>
-      <w>`.__T__rowRanges:DelayedArray`</w>
-      <w>`.__T__rowRanges&lt;-:SummarizedExperiment`</w>
-      <w>`.__T__rowSums:BiocGenerics`</w>
-      <w>`.__T__rowSums:base`</w>
-      <w>`.__T__rowids:BSgenome`</w>
-      <w>`.__T__rowmask:Biostrings`</w>
-      <w>`.__T__rowmask&lt;-:Biostrings`</w>
-      <w>`.__T__rownames:BiocGenerics`</w>
-      <w>`.__T__rownames&lt;-:base`</w>
-      <w>`.__T__rowpAUCs:genefilter`</w>
-      <w>`.__T__rowttests:genefilter`</w>
-      <w>`.__T__rtime:ProtGenerics`</w>
-      <w>`.__T__runLength:S4Vectors`</w>
-      <w>`.__T__runLength&lt;-:S4Vectors`</w>
-      <w>`.__T__runNames:ShortRead`</w>
-      <w>`.__T__runTest:topGO`</w>
-      <w>`.__T__runValue:S4Vectors`</w>
-      <w>`.__T__runValue&lt;-:S4Vectors`</w>
-      <w>`.__T__runmean:S4Vectors`</w>
-      <w>`.__T__runmed:stats`</w>
-      <w>`.__T__runq:S4Vectors`</w>
-      <w>`.__T__runsum:S4Vectors`</w>
-      <w>`.__T__runwtsum:S4Vectors`</w>
-      <w>`.__T__rvm:kernlab`</w>
-      <w>`.__T__sample:base`</w>
-      <w>`.__T__sampleLabels:CAGEr`</w>
-      <w>`.__T__sampleMap:MultiAssayExperiment`</w>
-      <w>`.__T__sampleMap&lt;-:MultiAssayExperiment`</w>
-      <w>`.__T__sampleNAs:methylumi`</w>
-      <w>`.__T__sampleNames:Biobase`</w>
-      <w>`.__T__sampleNames:MOFAtools`</w>
-      <w>`.__T__sampleNames&lt;-:Biobase`</w>
-      <w>`.__T__sampleNames&lt;-:MOFAtools`</w>
-      <w>`.__T__sampleRandom:raster`</w>
-      <w>`.__T__sampleRegular:raster`</w>
-      <w>`.__T__sampleStratified:raster`</w>
-      <w>`.__T__samples:Biobase`</w>
-      <w>`.__T__sampling:rstan`</w>
-      <w>`.__T__sandbag:scran`</w>
-      <w>`.__T__sapply:BiocGenerics`</w>
-      <w>`.__T__saveDb:AnnotationDbi`</w>
-      <w>`.__T__saveXML:XML`</w>
-      <w>`.__T__sc3:SC3`</w>
-      <w>`.__T__sc3_calc_biology:SC3`</w>
-      <w>`.__T__sc3_calc_consens:SC3`</w>
-      <w>`.__T__sc3_calc_dists:SC3`</w>
-      <w>`.__T__sc3_calc_transfs:SC3`</w>
-      <w>`.__T__sc3_estimate_k:SC3`</w>
-      <w>`.__T__sc3_export_results_xls:SC3`</w>
-      <w>`.__T__sc3_interactive:SC3`</w>
-      <w>`.__T__sc3_kmeans:SC3`</w>
-      <w>`.__T__sc3_plot_cluster_stability:SC3`</w>
-      <w>`.__T__sc3_plot_consensus:SC3`</w>
-      <w>`.__T__sc3_plot_de_genes:SC3`</w>
-      <w>`.__T__sc3_plot_expression:SC3`</w>
-      <w>`.__T__sc3_plot_markers:SC3`</w>
-      <w>`.__T__sc3_plot_silhouette:SC3`</w>
-      <w>`.__T__sc3_prepare:SC3`</w>
-      <w>`.__T__sc3_run_svm:SC3`</w>
-      <w>`.__T__scale:base`</w>
-      <w>`.__T__scaling:kernlab`</w>
-      <w>`.__T__scanBam:Rsamtools`</w>
-      <w>`.__T__scanBamHeader:Rsamtools`</w>
-      <w>`.__T__scanBcf:Rsamtools`</w>
-      <w>`.__T__scanBcfHeader:Rsamtools`</w>
-      <w>`.__T__scanFa:Rsamtools`</w>
-      <w>`.__T__scanFaIndex:Rsamtools`</w>
-      <w>`.__T__scanTabix:Rsamtools`</w>
-      <w>`.__T__scanVcf:VariantAnnotation`</w>
-      <w>`.__T__scanVcfHeader:VariantAnnotation`</w>
-      <w>`.__T__scans:ProtGenerics`</w>
-      <w>`.__T__scheme&lt;-:urltools`</w>
-      <w>`.__T__score:BiocGenerics`</w>
-      <w>`.__T__score&lt;-:BiocGenerics`</w>
-      <w>`.__T__scoreOrder:topGO`</w>
-      <w>`.__T__scorePlot:rrcov`</w>
-      <w>`.__T__scoreShift:CAGEr`</w>
-      <w>`.__T__scoresInTerm:topGO`</w>
-      <w>`.__T__screeplot:stats`</w>
-      <w>`.__T__sd:BiocGenerics`</w>
-      <w>`.__T__sd:sn`</w>
-      <w>`.__T__se.exprs:Biobase`</w>
-      <w>`.__T__se.exprs&lt;-:Biobase`</w>
-      <w>`.__T__seabi:wateRmelon`</w>
-      <w>`.__T__second:S4Vectors`</w>
-      <w>`.__T__second&lt;-:S4Vectors`</w>
-      <w>`.__T__second&lt;-:lubridate`</w>
-      <w>`.__T__sectionNames:beadarray`</w>
-      <w>`.__T__seed:DelayedArray`</w>
-      <w>`.__T__select:AnnotationDbi`</w>
-      <w>`.__T__select:raster`</w>
-      <w>`.__T__selectChannels:Biobase`</w>
-      <w>`.__T__selfmatch:S4Vectors`</w>
-      <w>`.__T__sens:genefilter`</w>
-      <w>`.__T__seqinfo:GenomeInfoDb`</w>
-      <w>`.__T__seqinfo&lt;-:GenomeInfoDb`</w>
-      <w>`.__T__seqlengths:GenomeInfoDb`</w>
-      <w>`.__T__seqlengths&lt;-:GenomeInfoDb`</w>
-      <w>`.__T__seqlevels0:GenomeInfoDb`</w>
-      <w>`.__T__seqlevels:GenomeInfoDb`</w>
-      <w>`.__T__seqlevels&lt;-:GenomeInfoDb`</w>
-      <w>`.__T__seqlevelsInUse:GenomeInfoDb`</w>
-      <w>`.__T__seqlevelsStyle:GenomeInfoDb`</w>
-      <w>`.__T__seqlevelsStyle&lt;-:GenomeInfoDb`</w>
-      <w>`.__T__seqnames:GenomeInfoDb`</w>
-      <w>`.__T__seqnames&lt;-:GenomeInfoDb`</w>
-      <w>`.__T__seqnamesTabix:Rsamtools`</w>
-      <w>`.__T__seqtype:Biostrings`</w>
-      <w>`.__T__seqtype&lt;-:Biostrings`</w>
-      <w>`.__T__sequenceReport:PWMEnrich`</w>
-      <w>`.__T__setCMethod:inline`</w>
-      <w>`.__T__setColors:CAGEr`</w>
-      <w>`.__T__setIdentifier:GSEABase`</w>
-      <w>`.__T__setIdentifier&lt;-:GSEABase`</w>
-      <w>`.__T__setInpBimapFilter:AnnotationDbi`</w>
-      <w>`.__T__setListElement:S4Vectors`</w>
-      <w>`.__T__setMinMax:raster`</w>
-      <w>`.__T__setName:GSEABase`</w>
-      <w>`.__T__setName&lt;-:GSEABase`</w>
-      <w>`.__T__setPar:Gviz`</w>
-      <w>`.__T__setTrackStyleParam:trackViewer`</w>
-      <w>`.__T__setTrackViewerStyleParam:trackViewer`</w>
-      <w>`.__T__setTrackXscaleParam:trackViewer`</w>
-      <w>`.__T__setTrackYaxisParam:trackViewer`</w>
-      <w>`.__T__setValues:raster`</w>
-      <w>`.__T__setVersion:GSEABase`</w>
-      <w>`.__T__setVersion&lt;-:GSEABase`</w>
-      <w>`.__T__setdiff:BiocGenerics`</w>
-      <w>`.__T__setdiff:base`</w>
-      <w>`.__T__setequal:base`</w>
-      <w>`.__T__setlist:systemPipeR`</w>
-      <w>`.__T__shape:Rgraphviz`</w>
-      <w>`.__T__shapefile:raster`</w>
-      <w>`.__T__shift:IRanges`</w>
-      <w>`.__T__shift:raster`</w>
-      <w>`.__T__shiftApply:S4Vectors`</w>
-      <w>`.__T__show:methods`</w>
-      <w>`.__T__showAsCell:S4Vectors`</w>
-      <w>`.__T__shrinkageFun:biovizBase`</w>
-      <w>`.__T__sidePage:annotate`</w>
-      <w>`.__T__sigAllMembers:topGO`</w>
-      <w>`.__T__sigCategories:Category`</w>
-      <w>`.__T__sigGenes:topGO`</w>
-      <w>`.__T__sigMembers:topGO`</w>
-      <w>`.__T__sigMembers&lt;-:topGO`</w>
-      <w>`.__T__sigRatio&lt;-:topGO`</w>
-      <w>`.__T__sigest:kernlab`</w>
-      <w>`.__T__signif:base`</w>
-      <w>`.__T__size:intervals`</w>
-      <w>`.__T__size:kernlab`</w>
-      <w>`.__T__sizeFactors:BiocGenerics`</w>
-      <w>`.__T__sizeFactors&lt;-:BiocGenerics`</w>
-      <w>`.__T__skewpart:Matrix`</w>
-      <w>`.__T__slice:IRanges`</w>
-      <w>`.__T__slidingWindows:IRanges`</w>
-      <w>`.__T__slotsFromS3:methods`</w>
-      <w>`.__T__smoothEnds:stats`</w>
-      <w>`.__T__snapshotDate:AnnotationHub`</w>
-      <w>`.__T__snapshotDate&lt;-:AnnotationHub`</w>
-      <w>`.__T__snpCall:Biobase`</w>
-      <w>`.__T__snpCall&lt;-:Biobase`</w>
-      <w>`.__T__snpCallProbability:Biobase`</w>
-      <w>`.__T__snpCallProbability&lt;-:Biobase`</w>
-      <w>`.__T__snpSummary:VariantAnnotation`</w>
-      <w>`.__T__snpcount:BSgenome`</w>
-      <w>`.__T__snpid2alleles:BSgenome`</w>
-      <w>`.__T__snpid2grange:BSgenome`</w>
-      <w>`.__T__snpid2loc:BSgenome`</w>
-      <w>`.__T__snplocs:BSgenome`</w>
-      <w>`.__T__snpsById:BSgenome`</w>
-      <w>`.__T__snpsByOverlaps:BSgenome`</w>
-      <w>`.__T__snpsBySeqname:BSgenome`</w>
-      <w>`.__T__snr:beadarray`</w>
-      <w>`.__T__softFilterMatrix:VariantAnnotation`</w>
-      <w>`.__T__softFilterMatrix&lt;-:VariantAnnotation`</w>
-      <w>`.__T__software:systemPipeR`</w>
-      <w>`.__T__solarnoon:maptools`</w>
-      <w>`.__T__solarpos:maptools`</w>
-      <w>`.__T__solve:base`</w>
-      <w>`.__T__solveCoef:MatrixModels`</w>
-      <w>`.__T__sort:BiocGenerics`</w>
-      <w>`.__T__sortBam:Rsamtools`</w>
-      <w>`.__T__sortSeqlevels:GenomeInfoDb`</w>
-      <w>`.__T__source:base`</w>
-      <w>`.__T__sourceUrl:BSgenome`</w>
-      <w>`.__T__sp.lineLabel:maptools`</w>
-      <w>`.__T__sp.pointLabel:maptools`</w>
-      <w>`.__T__sp:Rgraphviz`</w>
-      <w>`.__T__spCbind:maptools`</w>
-      <w>`.__T__spChFIDs:sp`</w>
-      <w>`.__T__spChFIDs&lt;-:sp`</w>
-      <w>`.__T__spRbind:maptools`</w>
-      <w>`.__T__spTransform:sp`</w>
-      <w>`.__T__space:S4Vectors`</w>
-      <w>`.__T__spam:spam`</w>
-      <w>`.__T__spatialIndex:BSgenome`</w>
-      <w>`.__T__spec:genefilter`</w>
-      <w>`.__T__specc:kernlab`</w>
-      <w>`.__T__species:BiocGenerics`</w>
-      <w>`.__T__species&lt;-:BiocGenerics`</w>
-      <w>`.__T__spectra:ProtGenerics`</w>
-      <w>`.__T__spikeNames:SingleCellExperiment`</w>
-      <w>`.__T__splines:Rgraphviz`</w>
-      <w>`.__T__split:base`</w>
-      <w>`.__T__split&lt;-:base`</w>
-      <w>`.__T__splitAsList:IRanges`</w>
-      <w>`.__T__splitByFacets:biovizBase`</w>
-      <w>`.__T__splitRanges:IRanges`</w>
-      <w>`.__T__sppanel:sp`</w>
-      <w>`.__T__spplot:sp`</w>
-      <w>`.__T__spsample:sp`</w>
-      <w>`.__T__sqlAppendTable:DBI`</w>
-      <w>`.__T__sqlCreateTable:DBI`</w>
-      <w>`.__T__sqlData:DBI`</w>
-      <w>`.__T__sqlInterpolate:DBI`</w>
-      <w>`.__T__sqlParseVariables:DBI`</w>
-      <w>`.__T__srFilter:ShortRead`</w>
-      <w>`.__T__srdistance:ShortRead`</w>
-      <w>`.__T__srduplicated:ShortRead`</w>
-      <w>`.__T__sread:ShortRead`</w>
-      <w>`.__T__srorder:ShortRead`</w>
-      <w>`.__T__srrank:ShortRead`</w>
-      <w>`.__T__srsort:ShortRead`</w>
-      <w>`.__T__stack:utils`</w>
-      <w>`.__T__stackSamples:VariantAnnotation`</w>
-      <w>`.__T__stackSelect:raster`</w>
-      <w>`.__T__stacking:Gviz`</w>
-      <w>`.__T__stacking&lt;-:Gviz`</w>
-      <w>`.__T__stacks:Gviz`</w>
-      <w>`.__T__stand_exprs:scater`</w>
-      <w>`.__T__stand_exprs&lt;-:scater`</w>
-      <w>`.__T__start:stats`</w>
-      <w>`.__T__start&lt;-:BiocGenerics`</w>
-      <w>`.__T__startElement.SAX:XML`</w>
-      <w>`.__T__startIndex:Biostrings`</w>
-      <w>`.__T__stats:ShortRead`</w>
-      <w>`.__T__storageMode:Biobase`</w>
-      <w>`.__T__storageMode&lt;-:Biobase`</w>
-      <w>`.__T__strand:BiocGenerics`</w>
-      <w>`.__T__strand&lt;-:BiocGenerics`</w>
-      <w>`.__T__strandMode:GenomicAlignments`</w>
-      <w>`.__T__strandMode&lt;-:GenomicAlignments`</w>
-      <w>`.__T__stringDist:Biostrings`</w>
-      <w>`.__T__strsplit:Biostrings`</w>
-      <w>`.__T__style:Rgraphviz`</w>
-      <w>`.__T__sub:base`</w>
-      <w>`.__T__subAxt:CNEr`</w>
-      <w>`.__T__subGraph:graph`</w>
-      <w>`.__T__subject:IRanges`</w>
-      <w>`.__T__subpatterns:Biostrings`</w>
-      <w>`.__T__subs:raster`</w>
-      <w>`.__T__subseq:XVector`</w>
-      <w>`.__T__subseq&lt;-:XVector`</w>
-      <w>`.__T__subset:base`</w>
-      <w>`.__T__subsetByAssay:MultiAssayExperiment`</w>
-      <w>`.__T__subsetByColData:MultiAssayExperiment`</w>
-      <w>`.__T__subsetByColumn:MultiAssayExperiment`</w>
-      <w>`.__T__subsetByFilter:S4Vectors`</w>
-      <w>`.__T__subsetByOverlaps:IRanges`</w>
-      <w>`.__T__subsetByRow:MultiAssayExperiment`</w>
-      <w>`.__T__subset_seed_as_array:DelayedArray`</w>
-      <w>`.__T__subsets:GSEABase`</w>
-      <w>`.__T__substr:base`</w>
-      <w>`.__T__substring:base`</w>
-      <w>`.__T__subviews:IRanges`</w>
-      <w>`.__T__sum:base`</w>
-      <w>`.__T__summarizeOverlaps:GenomicAlignments`</w>
-      <w>`.__T__summarizeVariants:VariantAnnotation`</w>
-      <w>`.__T__summary:base`</w>
-      <w>`.__T__sunriset:maptools`</w>
-      <w>`.__T__supportedFilters:AnnotationFilter`</w>
-      <w>`.__T__supportedSeqlevelsStyles:ensembldb`</w>
-      <w>`.__T__surfaceArea:sp`</w>
-      <w>`.__T__swan:wateRmelon`</w>
-      <w>`.__T__swap:CNEr`</w>
-      <w>`.__T__symCount:CNEr`</w>
-      <w>`.__T__symbol:Gviz`</w>
-      <w>`.__T__symbol&lt;-:Gviz`</w>
-      <w>`.__T__symbolize:grImport`</w>
-      <w>`.__T__symdif:raster`</w>
-      <w>`.__T__symmpart:Matrix`</w>
-      <w>`.__T__syntenicDotplot:CNEr`</w>
-      <w>`.__T__sysargs:systemPipeR`</w>
-      <w>`.__T__t:base`</w>
-      <w>`.__T__tRNAs:GenomicFeatures`</w>
-      <w>`.__T__table:BiocGenerics`</w>
-      <w>`.__T__tableName:rtracklayer`</w>
-      <w>`.__T__tableName&lt;-:rtracklayer`</w>
-      <w>`.__T__tableNames:rtracklayer`</w>
-      <w>`.__T__tables:ShortRead`</w>
-      <w>`.__T__tabulate:VariantAnnotation`</w>
-      <w>`.__T__tagClusters:CAGEr`</w>
-      <w>`.__T__tagname:AnnotationDbi`</w>
-      <w>`.__T__tags:Gviz`</w>
-      <w>`.__T__tail:utils`</w>
-      <w>`.__T__tapply:BiocGenerics`</w>
-      <w>`.__T__targetRanges:CNEr`</w>
-      <w>`.__T__targetSeqs:CNEr`</w>
-      <w>`.__T__targetsheader:systemPipeR`</w>
-      <w>`.__T__targetsin:systemPipeR`</w>
-      <w>`.__T__targetsout:systemPipeR`</w>
-      <w>`.__T__taxonomyId:AnnotationDbi`</w>
-      <w>`.__T__tb.width:Biostrings`</w>
-      <w>`.__T__tb:Biostrings`</w>
-      <w>`.__T__tcrossprod:base`</w>
-      <w>`.__T__technicalCV2:scran`</w>
-      <w>`.__T__termStat:topGO`</w>
-      <w>`.__T__testDirection:Category`</w>
-      <w>`.__T__testDirection&lt;-:Category`</w>
-      <w>`.__T__testName:Category`</w>
-      <w>`.__T__testName:topGO`</w>
-      <w>`.__T__testName&lt;-:topGO`</w>
-      <w>`.__T__testPairedEndBam:Rsamtools`</w>
-      <w>`.__T__testStatPar:topGO`</w>
-      <w>`.__T__testStatistic:topGO`</w>
-      <w>`.__T__text.SAX:XML`</w>
-      <w>`.__T__text:graphics`</w>
-      <w>`.__T__threeUTRsByTranscript:GenomicFeatures`</w>
-      <w>`.__T__threebands:IRanges`</w>
-      <w>`.__T__threshold:graph`</w>
-      <w>`.__T__thresholds:CNEr`</w>
-      <w>`.__T__thresholds:IHW`</w>
-      <w>`.__T__tic:ProtGenerics`</w>
-      <w>`.__T__tile:IRanges`</w>
-      <w>`.__T__timeDate:timeDate`</w>
-      <w>`.__T__time_length:lubridate`</w>
-      <w>`.__T__to:Rgraphviz`</w>
-      <w>`.__T__to:S4Vectors`</w>
-      <w>`.__T__toComplex:Biostrings`</w>
-      <w>`.__T__toDot:Rgraphviz`</w>
-      <w>`.__T__toDotR:graph`</w>
-      <w>`.__T__toFile:annotate`</w>
-      <w>`.__T__toGXL:graph`</w>
-      <w>`.__T__toGmt:GSEABase`</w>
-      <w>`.__T__toHTML:XML`</w>
-      <w>`.__T__toSAF:ensembldb`</w>
-      <w>`.__T__toString:base`</w>
-      <w>`.__T__toTable:AnnotationDbi`</w>
-      <w>`.__T__toeplitz:stats`</w>
-      <w>`.__T__toggleProbes:AnnotationDbi`</w>
-      <w>`.__T__togglefun:ShortRead`</w>
-      <w>`.__T__togglep:ShortRead`</w>
-      <w>`.__T__togglez:ShortRead`</w>
-      <w>`.__T__togroup:IRanges`</w>
-      <w>`.__T__togrouplength:IRanges`</w>
-      <w>`.__T__togrouprank:IRanges`</w>
-      <w>`.__T__tolower:base`</w>
-      <w>`.__T__topPage:annotate`</w>
-      <w>`.__T__tost:wateRmelon`</w>
-      <w>`.__T__total.intensity:methylumi`</w>
-      <w>`.__T__totalDepth:VariantAnnotation`</w>
-      <w>`.__T__total_correlation:dimRed`</w>
-      <w>`.__T__toupper:base`</w>
-      <w>`.__T__tpm:SingleCellExperiment`</w>
-      <w>`.__T__tpm&lt;-:SingleCellExperiment`</w>
-      <w>`.__T__traceplot:rstan`</w>
-      <w>`.__T__track:rtracklayer`</w>
-      <w>`.__T__track&lt;-:rtracklayer`</w>
-      <w>`.__T__trackName:rtracklayer`</w>
-      <w>`.__T__trackName&lt;-:rtracklayer`</w>
-      <w>`.__T__trackNames:rtracklayer`</w>
-      <w>`.__T__trackNames&lt;-:rtracklayer`</w>
-      <w>`.__T__transcript:Gviz`</w>
-      <w>`.__T__transcript&lt;-:Gviz`</w>
-      <w>`.__T__transcripts:GenomicFeatures`</w>
-      <w>`.__T__transcriptsBy:GenomicFeatures`</w>
-      <w>`.__T__transcriptsByOverlaps:GenomicFeatures`</w>
-      <w>`.__T__transform:base`</w>
-      <w>`.__T__transformToDf:biovizBase`</w>
-      <w>`.__T__transformToGenome:biovizBase`</w>
-      <w>`.__T__translate:Biostrings`</w>
-      <w>`.__T__treeLevels:Category`</w>
-      <w>`.__T__trendVar:scran`</w>
-      <w>`.__T__trigamma:base`</w>
-      <w>`.__T__tril:Matrix`</w>
-      <w>`.__T__trim:IRanges`</w>
-      <w>`.__T__trim:raster`</w>
-      <w>`.__T__trimEnds:ShortRead`</w>
-      <w>`.__T__trimLRPatterns:Biostrings`</w>
-      <w>`.__T__trimTails:ShortRead`</w>
-      <w>`.__T__trimTailw:ShortRead`</w>
-      <w>`.__T__triu:Matrix`</w>
-      <w>`.__T__truegain:kernlab`</w>
-      <w>`.__T__twoWayAlphabetFrequency:Biostrings`</w>
-      <w>`.__T__txtLabel:Rgraphviz`</w>
-      <w>`.__T__type:Biostrings`</w>
-      <w>`.__T__type:DelayedArray`</w>
-      <w>`.__T__type:intervals`</w>
-      <w>`.__T__type:kernlab`</w>
-      <w>`.__T__type&lt;-:intervals`</w>
-      <w>`.__T__ucscSchema:rtracklayer`</w>
-      <w>`.__T__ucscTableQuery:rtracklayer`</w>
-      <w>`.__T__ucscTrackModes:rtracklayer`</w>
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-      <w>aes_cbc_decrypt</w>
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-      <w>aes_ctr_decrypt</w>
-      <w>aes_ctr_encrypt</w>
-      <w>aes_gcm_decrypt</w>
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-      <w>aes_keygen</w>
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-      <w>aggregate</w>
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-      <w>agopen</w>
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-      <w>agraph</w>
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-      <w>agriculture</w>
-      <w>agwrite</w>
-      <w>ahead_behind</w>
-      <w>aic</w>
-      <w>aicplot</w>
-      <w>aids</w>
-      <w>aircondit</w>
-      <w>aircondit7</w>
-      <w>aircraft</w>
-      <w>airmay</w>
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-      <w>aveNumEdges</w>
-      <w>aveWithArgs</w>
-      <w>avearrays</w>
-      <w>avearrays.EList</w>
-      <w>avearrays.MAList</w>
-      <w>avearrays.default</w>
-      <w>avedups</w>
-      <w>avedups.EList</w>
-      <w>avedups.MAList</w>
-      <w>avedups.default</w>
-      <w>aver.wavefront</w>
-      <w>average.image</w>
-      <w>average.path.length</w>
-      <w>avereps</w>
-      <w>avereps.EList</w>
-      <w>avereps.EListRaw</w>
-      <w>avereps.MAList</w>
-      <w>avereps.RGList</w>
-      <w>avereps.default</w>
-      <w>awcoord</w>
-      <w>axTexpr</w>
-      <w>axTicks</w>
-      <w>axis</w>
-      <w>axis.Date</w>
-      <w>axis.POSIXct</w>
-      <w>axis.break</w>
-      <w>axis.default</w>
-      <w>axis.grid</w>
-      <w>axis.mult</w>
-      <w>axis.timeDate</w>
-      <w>axisPhylo</w>
-      <w>axisTicks</w>
-      <w>axisTrack</w>
-      <w>axis_canvas</w>
-      <w>axtChain</w>
-      <w>axtInfo</w>
-      <w>b</w>
-      <w>bLines</w>
-      <w>ba.game</w>
-      <w>baby</w>
-      <w>backGround</w>
-      <w>backSpline</w>
-      <w>backdoor</w>
-      <w>backgroundCorrect</w>
-      <w>backgroundCorrect.matrix</w>
-      <w>backgroundCorrectSingleSection</w>
-      <w>background_grid</w>
-      <w>background_image</w>
-      <w>backports</w>
-      <w>backsolve</w>
-      <w>backsolve.spam</w>
-      <w>backsolvet</w>
-      <w>backtick</w>
-      <w>backtrace</w>
-      <w>bacteria</w>
-      <w>bad</w>
-      <w>badDend</w>
-      <w>bag</w>
-      <w>bagControl</w>
-      <w>bagEarth</w>
-      <w>bagEarthStats</w>
-      <w>bagFDA</w>
-      <w>bagging</w>
-      <w>bake</w>
-      <w>balance</w>
-      <w>balanceMethodsList</w>
-      <w>balancedGrouped</w>
-      <w>ballocation</w>
-      <w>balloonplot</w>
-      <w>bam</w>
-      <w>bam.update</w>
-      <w>bamExperiment</w>
-      <w>bamFlag</w>
-      <w>bamFlagAND</w>
-      <w>bamFlagAsBitMatrix</w>
-      <w>bamFlagTest</w>
-      <w>bamIndicies</w>
-      <w>bamMapqFilter</w>
-      <w>bamPaths</w>
-      <w>bamRanges</w>
-      <w>bamReverseComplement</w>
-      <w>bamSamples</w>
-      <w>bamSimpleCigar</w>
-      <w>bamTag</w>
-      <w>bamTagFilter</w>
-      <w>bamWhat</w>
-      <w>bamWhich</w>
-      <w>band</w>
-      <w>bandSparse</w>
-      <w>band_instruments</w>
-      <w>band_instruments2</w>
-      <w>band_members</w>
-      <w>bandchol</w>
-      <w>bandnr</w>
-      <w>bandplot</w>
-      <w>bandwidth</w>
-      <w>bandwidth.kernel</w>
-      <w>bandwidth.nrd</w>
-      <w>bandwidth.rq</w>
-      <w>banking</w>
-      <w>banknote</w>
-      <w>banknoten</w>
-      <w>bannerplot</w>
-      <w>baptize</w>
-      <w>barNest</w>
-      <w>barabasi.game</w>
-      <w>barchart</w>
-      <w>barcodeplot</w>
-      <w>barlabels</w>
-      <w>barley</w>
-      <w>barolo</w>
-      <w>barp</w>
-      <w>barplot</w>
-      <w>barplot.ProbeSet</w>
-      <w>barplot.default</w>
-      <w>barplot2</w>
-      <w>barro</w>
-      <w>bartlett.test</w>
-      <w>bary2cart</w>
-      <w>base</w>
-      <w>base.freq</w>
-      <w>base64</w>
-      <w>base64Decode</w>
-      <w>base64Encode</w>
-      <w>base64_dec</w>
-      <w>base64_decode</w>
-      <w>base64_enc</w>
-      <w>base64_encode</w>
-      <w>base64decode</w>
-      <w>base64enc</w>
-      <w>base64encode</w>
-      <w>baseCallPath</w>
-      <w>baseOf</w>
-      <w>basePath</w>
-      <w>baseViewports</w>
-      <w>baseball</w>
-      <w>baseenv</w>
-      <w>basehaz</w>
-      <w>basename</w>
-      <w>bash</w>
-      <w>basicHeaderGatherer</w>
-      <w>basicPage</w>
-      <w>basicPower</w>
-      <w>basicPowerAxis</w>
-      <w>basicTextGatherer</w>
-      <w>bassAckward</w>
-      <w>bassAckward.diagram</w>
-      <w>batchExpandGrid</w>
-      <w>batchExport</w>
-      <w>batchMap</w>
-      <w>batchMapQuick</w>
-      <w>batchMapResults</w>
-      <w>batchQuery</w>
-      <w>batchReduce</w>
-      <w>batchReduceResults</w>
-      <w>batchSE</w>
-      <w>batchSOM</w>
-      <w>batchUnexport</w>
-      <w>batchsizes</w>
-      <w>batcoord</w>
-      <w>battleship.plot</w>
-      <w>batvarcoord</w>
-      <w>bayes_R2</w>
-      <w>bbatch</w>
-      <w>bbexpand</w>
-      <w>bbox</w>
-      <w>bc</w>
-      <w>bcCategory</w>
-      <w>bcPower</w>
-      <w>bcPowerAxis</w>
-      <w>bcSubCategory</w>
-      <w>bcfFixed</w>
-      <w>bcfGeno</w>
-      <w>bcfInfo</w>
-      <w>bcfMode</w>
-      <w>bcfSamples</w>
-      <w>bcfTrimEmpty</w>
-      <w>bcfWhich</w>
-      <w>bclust</w>
-      <w>bcnPower</w>
-      <w>bcnPowerAxis</w>
-      <w>bcnPowerInverse</w>
-      <w>bcrypt_pbkdf</w>
-      <w>bcv</w>
-      <w>bd.ext</w>
-      <w>bd.time</w>
-      <w>bdf</w>
-      <w>bdiag</w>
-      <w>bdiag.spam</w>
-      <w>beachmat</w>
-      <w>beadCountWeights</w>
-      <w>beadNum</w>
-      <w>beadStatusVector</w>
-      <w>beadarray</w>
-      <w>beadarrayUsersGuide</w>
-      <w>beadc</w>
-      <w>beadcount</w>
-      <w>beamer_presentation</w>
-      <w>beanplot</w>
-      <w>beav1</w>
-      <w>beav2</w>
-      <w>beaver</w>
-      <w>beckerp</w>
-      <w>beeswarm</w>
-      <w>beets</w>
-      <w>beginCluster</w>
-      <w>bellman.ford.sp</w>
-      <w>bench_tbls</w>
-      <w>benchplot</w>
-      <w>bernhardsson</w>
-      <w>bernhardssonA</w>
-      <w>bernhardssonB</w>
-      <w>besselI</w>
-      <w>besselJ</w>
-      <w>besselK</w>
-      <w>besselY</w>
-      <w>besseldot</w>
-      <w>best</w>
-      <w>best.nnet</w>
-      <w>best.randomForest</w>
-      <w>best.rpart</w>
-      <w>best.svm</w>
-      <w>best.tune</w>
-      <w>bestItems</w>
-      <w>bestScales</w>
-      <w>beta</w>
-      <w>beta.lvm</w>
-      <w>beta2m</w>
-      <w>betaBinomialGLM</w>
-      <w>betaEst</w>
-      <w>betaEstMultiple</w>
-      <w>betaObjf</w>
-      <w>beta_real</w>
-      <w>betablocker</w>
-      <w>betabreaker</w>
-      <w>betaqn</w>
-      <w>betar</w>
-      <w>betas</w>
-      <w>between</w>
-      <w>betweenness</w>
-      <w>betweenness.centrality.clustering</w>
-      <w>betweenness.estimate</w>
-      <w>bezier</w>
-      <w>bezierGrob</w>
-      <w>bezierPoints</w>
-      <w>bfi</w>
-      <w>bfi.dictionary</w>
-      <w>bfp</w>
-      <w>bfs</w>
-      <w>bg.adjust</w>
-      <w>bg.correct</w>
-      <w>bg.correct.mas</w>
-      <w>bg.correct.none</w>
-      <w>bg.correct.rma</w>
-      <w>bg.parameters</w>
-      <w>bgAdjust</w>
-      <w>bgAdjustMethylation</w>
-      <w>bgBlack</w>
-      <w>bgBlue</w>
-      <w>bgCyan</w>
-      <w>bgGreen</w>
-      <w>bgIntensitySwan.methylumi</w>
-      <w>bgMagenta</w>
-      <w>bgRed</w>
-      <w>bgWhite</w>
-      <w>bgYellow</w>
-      <w>bg_black</w>
-      <w>bg_blue</w>
-      <w>bg_cyan</w>
-      <w>bg_green</w>
-      <w>bg_magenta</w>
-      <w>bg_red</w>
-      <w>bg_white</w>
-      <w>bg_yellow</w>
-      <w>bgcolor</w>
-      <w>bgcorrect.illumina</w>
-      <w>bgcorrect.methods</w>
-      <w>bgtest</w>
-      <w>bgzip</w>
-      <w>bgzipTabix</w>
-      <w>bh</w>
-      <w>bhattacharyya.dist</w>
-      <w>bhattacharyya.matrix</w>
-      <w>bi.bars</w>
-      <w>bi2int</w>
-      <w>biConnComp</w>
-      <w>biVar</w>
-      <w>bibcoupling</w>
-      <w>bibentry</w>
-      <w>bibentry_key</w>
-      <w>bibstyle</w>
-      <w>bibtex</w>
-      <w>bic</w>
-      <w>bicEMtrain</w>
-      <w>biconnected.components</w>
-      <w>biconnected_components</w>
-      <w>bifactor</w>
-      <w>bigcity</w>
-      <w>bignum</w>
-      <w>bignum_mod_exp</w>
-      <w>bignum_mod_inv</w>
-      <w>bin.wind.records</w>
-      <w>binCounts</w>
-      <w>binFromCoordRange</w>
-      <w>binMeanVar</w>
-      <w>binMeans</w>
-      <w>binPack</w>
-      <w>binRangesFromCoordRange</w>
-      <w>binRestrictionString</w>
-      <w>binaryBuffer</w>
-      <w>binaryPGLMM</w>
-      <w>binaryPGLMM.sim</w>
-      <w>binciW</w>
-      <w>binciWl</w>
-      <w>binciWu</w>
-      <w>bincombinations</w>
-      <w>binconf</w>
-      <w>bind</w>
-      <w>bind.tree</w>
-      <w>bindAsGRanges</w>
-      <w>bindData</w>
-      <w>bind_cols</w>
-      <w>bind_rows</w>
-      <w>bindingIsActive</w>
-      <w>bindingIsLocked</w>
-      <w>bindr</w>
-      <w>bindrcpp</w>
-      <w>bindtextdomain</w>
-      <w>binnedAverage</w>
-      <w>binom.test</w>
-      <w>binomTest</w>
-      <w>binomial</w>
-      <w>binomial.lvm</w>
-      <w>binomial.rd</w>
-      <w>binomial.rr</w>
-      <w>binomialGoodnessOfFit</w>
-      <w>binsearch</w>
-      <w>bioChemists</w>
-      <w>biocAccess</w>
-      <w>biocLite</w>
-      <w>biocRepos</w>
-      <w>biocUpdatePackages</w>
-      <w>biocValid</w>
-      <w>biocVersion</w>
-      <w>bioc_install_repos</w>
-      <w>biocases_group</w>
-      <w>biocinstallRepos</w>
-      <w>biomTrack</w>
-      <w>biomaRt</w>
-      <w>biomass</w>
-      <w>biomassTill</w>
-      <w>biomed</w>
-      <w>bionj</w>
-      <w>bionjs</w>
-      <w>biopsy</w>
-      <w>biovizBase</w>
-      <w>bipartite</w>
-      <w>bipartite.mapping</w>
-      <w>bipartite.projection</w>
-      <w>bipartite.projection.size</w>
-      <w>bipartite.random.game</w>
-      <w>bipartite_graph</w>
-      <w>bipartite_mapping</w>
-      <w>bipartite_projection</w>
-      <w>bipartite_projection_size</w>
-      <w>biplot</w>
-      <w>biplot.pcoa</w>
-      <w>biplot.psych</w>
-      <w>biquartimin</w>
-      <w>bird.families</w>
-      <w>bird.orders</w>
-      <w>birthdeath</w>
-      <w>birthwt</w>
-      <w>bisection.search</w>
-      <w>biserial</w>
-      <w>bit</w>
-      <w>bitAnd</w>
-      <w>bitFlip</w>
-      <w>bitOr</w>
-      <w>bitShiftL</w>
-      <w>bitShiftR</w>
-      <w>bitXor</w>
-      <w>bit_done</w>
-      <w>bit_init</w>
-      <w>bitmap</w>
-      <w>bitops</w>
-      <w>bitsplits</w>
-      <w>bitwAnd</w>
-      <w>bitwNot</w>
-      <w>bitwOr</w>
-      <w>bitwShiftL</w>
-      <w>bitwShiftR</w>
-      <w>bitwXor</w>
-      <w>bitwhich</w>
-      <w>biv.nt.prob</w>
-      <w>bkde</w>
-      <w>bkde2D</w>
-      <w>bkfe</w>
-      <w>bl.string</w>
-      <w>black</w>
-      <w>bladder</w>
-      <w>blake2b</w>
-      <w>blake2s</w>
-      <w>blame</w>
-      <w>blant</w>
-      <w>blastSequences</w>
-      <w>blatCNE</w>
-      <w>blc</w>
-      <w>blcInitializeSplitDichotomizeUsingMean</w>
-      <w>blcInitializeSplitEigen</w>
-      <w>blcInitializeSplitFanny</w>
-      <w>blcInitializeSplitHClust</w>
-      <w>blcSplit</w>
-      <w>blcSplitCriterionBIC</w>
-      <w>blcSplitCriterionBICICL</w>
-      <w>blcSplitCriterionJustRecordEverything</w>
-      <w>blcSplitCriterionLRT</w>
-      <w>blcSplitCriterionLevelWtdBIC</w>
-      <w>blcSubTree</w>
-      <w>blcTree</w>
-      <w>blcTreeApply</w>
-      <w>blcTreeLeafClasses</w>
-      <w>blcTreeLeafMatrix</w>
-      <w>blcTreeOverallBIC</w>
-      <w>blind.pal.info</w>
-      <w>blob</w>
-      <w>blob_create</w>
-      <w>block.random</w>
-      <w>blockDiag</w>
-      <w>blockEnd</w>
-      <w>blockFX</w>
-      <w>blockFinder</w>
-      <w>blockGraphs</w>
-      <w>blockSize</w>
-      <w>blockStart</w>
-      <w>blockdiag</w>
-      <w>blocks</w>
-      <w>blocksizes</w>
-      <w>bloodtransfusion</w>
-      <w>blot</w>
-      <w>blue</w>
-      <w>bluered</w>
-      <w>blues9</w>
-      <w>blurred</w>
-      <w>bmTrack</w>
-      <w>bmd</w>
-      <w>bmidata</w>
-      <w>bmp</w>
-      <w>bobyqa</w>
-      <w>body</w>
-      <w>bold</w>
-      <w>bondyield</w>
-      <w>bonpow</w>
-      <w>bookmarkButton</w>
-      <w>boot</w>
-      <w>boot.array</w>
-      <w>boot.ci</w>
-      <w>boot.comp</w>
-      <w>boot.crq</w>
-      <w>boot.null</w>
-      <w>boot.phylo</w>
-      <w>boot.resample</w>
-      <w>boot.rq</w>
-      <w>boot.rq.mcmb</w>
-      <w>boot.rq.pwy</w>
-      <w>boot.rq.spwy</w>
-      <w>boot.rq.wxy</w>
-      <w>boot.rq.xy</w>
-      <w>boot.se</w>
-      <w>bootCase</w>
-      <w>bootdist</w>
-      <w>bootdistcens</w>
-      <w>bootest</w>
-      <w>bootkm</w>
-      <w>bootstrap</w>
-      <w>bootstrap.enrichment.test</w>
-      <w>bootstrap.lca</w>
-      <w>bootstrapLib</w>
-      <w>bootstrapPage</w>
-      <w>bootstrapPairs</w>
-      <w>bootstrap_moby</w>
-      <w>bootstrap_p</w>
-      <w>bootstrap_p_moby</w>
-      <w>bootstraps</w>
-      <w>border</w>
-      <w>borders</w>
-      <w>bosTau2.geneSymbol.LENGTH</w>
-      <w>bosTau2.geneid.LENGTH</w>
-      <w>bosTau2.genscan.LENGTH</w>
-      <w>bosTau2.refGene.LENGTH</w>
-      <w>bosTau2.sgpGene.LENGTH</w>
-      <w>bosTau3.ensGene.LENGTH</w>
-      <w>bosTau3.geneSymbol.LENGTH</w>
-      <w>bosTau3.geneid.LENGTH</w>
-      <w>bosTau3.genscan.LENGTH</w>
-      <w>bosTau3.refGene.LENGTH</w>
-      <w>bosTau3.sgpGene.LENGTH</w>
-      <w>bosTau4.ensGene.LENGTH</w>
-      <w>bosTau4.geneSymbol.LENGTH</w>
-      <w>bosTau4.genscan.LENGTH</w>
-      <w>bosTau4.nscanGene.LENGTH</w>
-      <w>bosTau4.refGene.LENGTH</w>
-      <w>botLeft</w>
-      <w>boundBox</w>
-      <w>boundaries</w>
-      <w>boundary</w>
-      <w>boundedClusterMaker</w>
-      <w>box</w>
-      <w>box.cox</w>
-      <w>box.cox.powers</w>
-      <w>box.cox.var</w>
-      <w>box.heresy</w>
-      <w>box.tidwell</w>
-      <w>boxCox</w>
-      <w>boxCox2d</w>
-      <w>boxCoxVariable</w>
-      <w>boxTidwell</w>
-      <w>boxcox</w>
-      <w>boxcox_trans</w>
-      <w>boxed.labels</w>
-      <w>boxplot</w>
-      <w>boxplot.default</w>
-      <w>boxplot.matrix</w>
-      <w>boxplot.stats</w>
-      <w>boxplot2</w>
-      <w>boxplotColorBias</w>
-      <w>boxplotVGram</w>
-      <w>boxx</w>
-      <w>boyerMyrvoldPlanarityTest</w>
-      <w>bpRNGseed</w>
-      <w>bpaggregate</w>
-      <w>bpbackend</w>
-      <w>bpcatchErrors</w>
-      <w>bpisup</w>
-      <w>bpiterate</w>
-      <w>bpjobname</w>
-      <w>bplapply</w>
-      <w>bplasterror</w>
-      <w>bplog</w>
-      <w>bplogdir</w>
-      <w>bploop</w>
-      <w>bplot</w>
-      <w>bplot.xy</w>
-      <w>bpmapply</w>
-      <w>bpnworkers</w>
-      <w>bpok</w>
-      <w>bpower</w>
-      <w>bpower.sim</w>
-      <w>bpparam</w>
-      <w>bpplot</w>
-      <w>bpplotM</w>
-      <w>bpplt</w>
-      <w>bppltp</w>
-      <w>bpprogressbar</w>
-      <w>bpresultdir</w>
-      <w>bpresume</w>
-      <w>bprunMPIslave</w>
-      <w>bpschedule</w>
-      <w>bpstart</w>
-      <w>bpstop</w>
-      <w>bpstopOnError</w>
-      <w>bptasks</w>
-      <w>bptest</w>
-      <w>bpthreshold</w>
-      <w>bptimeout</w>
-      <w>bptry</w>
-      <w>bpvalidate</w>
-      <w>bpvec</w>
-      <w>bpvectorize</w>
-      <w>bpworkers</w>
-      <w>bpx</w>
-      <w>bpy.colors</w>
-      <w>bquote</w>
-      <w>br</w>
-      <w>braFlo1.xenoRefGene.LENGTH</w>
-      <w>brambles</w>
-      <w>branch_create</w>
-      <w>branch_delete</w>
-      <w>branch_get_upstream</w>
-      <w>branch_remote_name</w>
-      <w>branch_remote_url</w>
-      <w>branch_rename</w>
-      <w>branch_set_upstream</w>
-      <w>branch_target</w>
-      <w>branches</w>
-      <w>branches_attr_by_clusters</w>
-      <w>branches_attr_by_labels</w>
-      <w>branches_attr_by_lists</w>
-      <w>branches_color</w>
-      <w>branching.times</w>
-      <w>brandes.betweenness.centrality</w>
-      <w>break</w>
-      <w>breakInChunks</w>
-      <w>breakTies</w>
-      <w>breakpoints</w>
-      <w>breast</w>
-      <w>breast_cancer_wisconsin</w>
-      <w>breslow</w>
-      <w>brew</w>
-      <w>brewCache</w>
-      <w>brewCacheOff</w>
-      <w>brewCacheOn</w>
-      <w>brew_colors</w>
-      <w>brewer.pal</w>
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-      <w>browseUCSCtrack</w>
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-      <w>browserViewer</w>
-      <w>browserViews</w>
-      <w>brushOpts</w>
-      <w>brushedPoints</w>
-      <w>bs</w>
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-      <w>bsapply</w>
-      <w>bscols</w>
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-      <w>bscon_minfi</w>
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-      <w>bugs2jags</w>
-      <w>build</w>
-      <w>build.charmatrix</w>
-      <w>build.ext.nblist</w>
-      <w>build.nblist</w>
-      <w>buildChromLocation</w>
-      <w>buildEdgeList</w>
-      <w>buildLevels</w>
-      <w>buildNodeList</w>
-      <w>buildPubMedAbst</w>
-      <w>buildRepDepGraph</w>
-      <w>buildSNNGraph</w>
-      <w>buildToolsCheck</w>
-      <w>buildToolsExec</w>
-      <w>buildToolsInstall</w>
-      <w>buildVignette</w>
-      <w>buildVignettes</w>
-      <w>build_ah_annots</w>
-      <w>build_annotations</w>
-      <w>build_manual</w>
-      <w>build_readme</w>
-      <w>build_site</w>
-      <w>build_snp_location_tables.r</w>
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-      <w>build_vignettes</w>
-      <w>build_win</w>
-      <w>builtin_annotations</w>
-      <w>builtin_genomes</w>
-      <w>builtins</w>
-      <w>bumpchart</w>
-      <w>bumphunter</w>
-      <w>bumphunterEngine</w>
-      <w>bumps</w>
-      <w>bundle_r_package</w>
-      <w>bunzip2</w>
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-      <w>bupa</w>
-      <w>burt</w>
-      <w>bus</w>
-      <w>bushfire</w>
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-      <w>button</w>
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-      <w>bvh</w>
-      <w>bvpost.optim</w>
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-      <w>bvstart.vals</w>
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-      <w>bw.nrd</w>
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-      <w>bw.ucv</w>
-      <w>bwplot</w>
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-      <w>bwss.matrix</w>
-      <w>bxp</w>
-      <w>bxplot</w>
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-      <w>bystats</w>
-      <w>bystats2</w>
-      <w>bzfile</w>
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-      <w>cabbages</w>
-      <w>cache</w>
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-      <w>cacheMetaData</w>
-      <w>cacheMethod</w>
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-      <w>cache_filesystem</w>
-      <w>cache_info</w>
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-      <w>caith</w>
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-      <w>calJac1.nscanGene.LENGTH</w>
-      <w>calJac1.xenoRefGene.LENGTH</w>
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-      <w>calculateVarianceExplained</w>
-      <w>calculate_celltype_associations</w>
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-      <w>cameraPR.default</w>
-      <w>can</w>
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-      <w>canFam1.geneSymbol.LENGTH</w>
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-      <w>canFam1.nscanGene.LENGTH</w>
-      <w>canFam1.refGene.LENGTH</w>
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-      <w>canFam2.ensGene.LENGTH</w>
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-      <w>canFam2.refGene.LENGTH</w>
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-      <w>capabilities</w>
-      <w>capability</w>
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-      <w>capitalizeStrings</w>
-      <w>caption</w>
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-      <w>captureOutput</w>
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-      <w>cars</w>
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-      <w>cat_line</w>
-      <w>cat_print</w>
-      <w>cat_rule</w>
-      <w>catalogAdd</w>
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-      <w>catalogDump</w>
-      <w>catalogLoad</w>
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-      <w>catch</w>
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-      <w>catf</w>
-      <w>catlist</w>
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-      <w>cats</w>
-      <w>catsM</w>
-      <w>cattell</w>
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-      <w>cavPor3.genscan.LENGTH</w>
-      <w>cavPor3.nscanGene.LENGTH</w>
-      <w>cavPor3.xenoRefGene.LENGTH</w>
-      <w>cb1.xenoRefGene.LENGTH</w>
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-      <w>cb_contingency</w>
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-      <w>cb_parse_band_Mm</w>
-      <w>cb_sigBands</w>
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-      <w>cbind.CompressedMatrix</w>
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-      <w>cbind.DNAbin</w>
-      <w>cbind.DataFrame</w>
-      <w>cbind.EList</w>
-      <w>cbind.EListRaw</w>
-      <w>cbind.MAList</w>
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-      <w>cbind.marrayNorm</w>
-      <w>cbind.marrayRaw</w>
-      <w>cbind.matrix.csr</w>
-      <w>cbind.spam</w>
-      <w>cbind.zoo</w>
-      <w>cbind2</w>
-      <w>cbindX</w>
-      <w>cbreaks</w>
-      <w>cc.genes</w>
-      <w>ccat</w>
-      <w>ccbvevd</w>
-      <w>ccf</w>
-      <w>cch</w>
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-      <w>cdbw</w>
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-      <w>cdensX</w>
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-      <w>cdfFromBioC</w>
-      <w>cdfFromEnvironment</w>
-      <w>cdfFromLibPath</w>
-      <w>cdfMclust</w>
-      <w>cdfName</w>
-      <w>cdfcomp</w>
-      <w>cdfcompcens</w>
-      <w>cdfenv.example</w>
-      <w>cdplot</w>
-      <w>cds</w>
-      <w>cdsBy</w>
-      <w>cdsByOverlaps</w>
-      <w>ce</w>
-      <w>ce2.geneSymbol.LENGTH</w>
-      <w>ce2.geneid.LENGTH</w>
-      <w>ce2.refGene.LENGTH</w>
-      <w>ce4.geneSymbol.LENGTH</w>
-      <w>ce4.refGene.LENGTH</w>
-      <w>ce4.xenoRefGene.LENGTH</w>
-      <w>ce6.ensGene.LENGTH</w>
-      <w>ce6.geneSymbol.LENGTH</w>
-      <w>ce6.refGene.LENGTH</w>
-      <w>ce6.xenoRefGene.LENGTH</w>
-      <w>ceScan</w>
-      <w>ceil</w>
-      <w>ceiling</w>
-      <w>ceiling2</w>
-      <w>ceiling_date</w>
-      <w>cellFromCol</w>
-      <w>cellFromLine</w>
-      <w>cellFromPolygon</w>
-      <w>cellFromRow</w>
-      <w>cellFromRowCol</w>
-      <w>cellFromRowColCombine</w>
-      <w>cellFromXY</w>
-      <w>cellStats</w>
-      <w>cell_addr</w>
-      <w>cell_cols</w>
-      <w>cell_limits</w>
-      <w>cell_rows</w>
-      <w>cellranger</w>
-      <w>cellsFromExtent</w>
-      <w>cement</w>
-      <w>censboot</w>
-      <w>censor</w>
-      <w>censored.fit</w>
-      <w>center.only</w>
-      <w>center.scale</w>
-      <w>centerText</w>
-      <w>centers</w>
-      <w>centers.bclust</w>
-      <w>centipede.plot</w>
-      <w>centr_betw</w>
-      <w>centr_betw_tmax</w>
-      <w>centr_clo</w>
-      <w>centr_clo_tmax</w>
-      <w>centr_degree</w>
-      <w>centr_degree_tmax</w>
-      <w>centr_eigen</w>
-      <w>centr_eigen_tmax</w>
-      <w>centralization.betweenness</w>
-      <w>centralization.betweenness.tmax</w>
-      <w>centralization.closeness</w>
-      <w>centralization.closeness.tmax</w>
-      <w>centralization.degree</w>
-      <w>centralization.degree.tmax</w>
-      <w>centralization.evcent</w>
-      <w>centralization.evcent.tmax</w>
-      <w>centralize</w>
-      <w>centralize.scores</w>
-      <w>ceres.plot</w>
-      <w>ceres.plots</w>
-      <w>ceresPlot</w>
-      <w>ceresPlots</w>
-      <w>cert_verify</w>
-      <w>cfBrewTemplate</w>
-      <w>cfHandleUnknownSubmitError</w>
-      <w>cfKillBatchJob</w>
-      <w>cfReadBrewTemplate</w>
-      <w>cforestStats</w>
-      <w>cfunction</w>
-      <w>cgd</w>
-      <w>cgetAnywhere</w>
-      <w>cgrestandard</w>
-      <w>chainMergeSort</w>
-      <w>chainNetSyntenic</w>
-      <w>chainPreNet</w>
-      <w>champ.Block</w>
-      <w>champ.CNA</w>
-      <w>champ.DMP</w>
-      <w>champ.DMR</w>
-      <w>champ.EpiMod</w>
-      <w>champ.GSEA</w>
-      <w>champ.QC</w>
-      <w>champ.SVD</w>
-      <w>champ.filter</w>
-      <w>champ.import</w>
-      <w>champ.impute</w>
-      <w>champ.load</w>
-      <w>champ.norm</w>
-      <w>champ.process</w>
-      <w>champ.refbase</w>
-      <w>champ.runCombat</w>
-      <w>chanames</w>
-      <w>change.origin</w>
-      <w>changeLog</w>
-      <w>change_palette</w>
-      <w>changedFiles</w>
-      <w>changes</w>
-      <w>channel</w>
-      <w>channelNames</w>
-      <w>channing</w>
-      <w>char.expand</w>
-      <w>char2Rdpiece</w>
-      <w>char2dms</w>
-      <w>char2numeric</w>
-      <w>charToInt</w>
-      <w>charToInt.default</w>
-      <w>charToRaw</w>
-      <w>character</w>
-      <w>character.table</w>
-      <w>characterToBSGenome</w>
-      <w>characterize</w>
-      <w>charmap</w>
-      <w>charmatch</w>
-      <w>chars8bit</w>
-      <w>charset_to_Unicode</w>
-      <w>chartr</w>
-      <w>chazuh</w>
-      <w>check</w>
-      <w>check.Assert</w>
-      <w>check.Rdoc</w>
-      <w>check.cdf.type</w>
-      <w>check.derivatives</w>
-      <w>check.ewce.genelist.inputs</w>
-      <w>check.options</w>
-      <w>check.species</w>
-      <w>checkAlignment</w>
-      <w>checkArg</w>
-      <w>checkArgs</w>
-      <w>checkAtAssignment</w>
-      <w>checkAttrs</w>
-      <w>checkBimodality</w>
-      <w>checkCRAN</w>
-      <w>checkCauses</w>
-      <w>checkCluster</w>
-      <w>checkConditionalX</w>
-      <w>checkConstraint</w>
-      <w>checkDocFiles</w>
-      <w>checkDocStyle</w>
-      <w>checkEquals</w>
-      <w>checkEqualsNumeric</w>
-      <w>checkException</w>
-      <w>checkFF</w>
-      <w>checkForRemoteErrors</w>
-      <w>checkGeneSymbols</w>
-      <w>checkIdentical</w>
-      <w>checkIds</w>
-      <w>checkInstall</w>
-      <w>checkLabel</w>
-      <w>checkListElementClass</w>
-      <w>checkMAPCOUNTS</w>
-      <w>checkMD5sums</w>
-      <w>checkModelName</w>
-      <w>checkNEWS</w>
-      <w>checkPlatform</w>
-      <w>checkPlot</w>
-      <w>checkPoFile</w>
-      <w>checkPoFiles</w>
-      <w>checkPolygonsHoles</w>
-      <w>checkRNG</w>
-      <w>checkRVersion</w>
-      <w>checkRd</w>
-      <w>checkRdaFiles</w>
-      <w>checkRegistration</w>
-      <w>checkReplaceFuns</w>
-      <w>checkResamples</w>
-      <w>checkS3methods</w>
-      <w>checkSlotAssignment</w>
-      <w>checkTargetInfo</w>
-      <w>checkTnF</w>
-      <w>checkTrue</w>
-      <w>checkUTF8</w>
-      <w>checkUsage</w>
-      <w>checkUsageEnv</w>
-      <w>checkUsagePackage</w>
-      <w>checkValidFilenames</w>
-      <w>checkValidPhylo</w>
-      <w>checkVignettes</w>
-      <w>checkWarning</w>
-      <w>check_bioc</w>
-      <w>check_build_tools</w>
-      <w>check_built</w>
-      <w>check_cols</w>
-      <w>check_compiler</w>
-      <w>check_cran</w>
-      <w>check_dbplyr</w>
-      <w>check_dep_version</w>
-      <w>check_details</w>
-      <w>check_divergences</w>
-      <w>check_dots_unnamed</w>
-      <w>check_dots_used</w>
-      <w>check_energy</w>
-      <w>check_failures</w>
-      <w>check_field</w>
-      <w>check_github</w>
-      <w>check_gitlab</w>
-      <w>check_hmc_diagnostics</w>
-      <w>check_inputs_to_magma_celltype_analysis</w>
-      <w>check_latex</w>
-      <w>check_man</w>
-      <w>check_missing</w>
-      <w>check_mnsl</w>
-      <w>check_name</w>
-      <w>check_packages_in_dir</w>
-      <w>check_packages_in_dir_changes</w>
-      <w>check_packages_in_dir_details</w>
-      <w>check_r</w>
-      <w>check_range</w>
-      <w>check_rhub</w>
-      <w>check_rtools</w>
-      <w>check_suggested</w>
-      <w>check_treedepth</w>
-      <w>check_type</w>
-      <w>check_tzones</w>
-      <w>check_win_devel</w>
-      <w>check_win_oldrelease</w>
-      <w>check_win_release</w>
-      <w>checkbox</w>
-      <w>checkboxGroupInput</w>
-      <w>checkboxInput</w>
-      <w>checkout</w>
-      <w>chem</w>
-      <w>chemdiab</w>
-      <w>chemdiab_1vs2</w>
-      <w>chemdiab_1vs3</w>
-      <w>chemdiab_2vs3</w>
-      <w>cherry</w>
-      <w>chevron</w>
-      <w>chgDefaults</w>
-      <w>chgroup</w>
-      <w>chi2r</w>
-      <w>chiSquare</w>
-      <w>chickwts</w>
-      <w>childNames</w>
-      <w>children</w>
-      <w>childrenOf</w>
-      <w>chiplot</w>
-      <w>chiroptera</w>
-      <w>chisq.ebam</w>
-      <w>chisq.lvm</w>
-      <w>chisq.stat</w>
-      <w>chisq.test</w>
-      <w>chisqClass</w>
-      <w>chkDots</w>
-      <w>chmatch</w>
-      <w>choicevar</w>
-      <w>chol</w>
-      <w>chol.default</w>
-      <w>chol.spam</w>
-      <w>chol2inv</w>
-      <w>chol2inv.spam</w>
-      <w>choldrop</w>
-      <w>cholest</w>
-      <w>cholup</w>
-      <w>choose</w>
-      <w>chooseBioCmirror</w>
-      <w>chooseCRANmirror</w>
-      <w>chooseCentralOrgPkgSymbol</w>
-      <w>choose_color</w>
-      <w>choose_palette</w>
-      <w>chorSub</w>
-      <w>chordal_ring</w>
-      <w>chorder</w>
-      <w>chr</w>
-      <w>chrCats</w>
-      <w>chrGraph</w>
-      <w>chrSelectBSseq</w>
-      <w>chrobakPayneStraightLineDrawing</w>
-      <w>chrom</w>
-      <w>chromInfo</w>
-      <w>chromLengths</w>
-      <w>chromLocs</w>
-      <w>chromNames</w>
-      <w>chroma_slice</w>
-      <w>chromatogram</w>
-      <w>chromatograms</w>
-      <w>chromosome</w>
-      <w>chromosomeFilter</w>
-      <w>chronoMPL</w>
-      <w>chronopl</w>
-      <w>chronos</w>
-      <w>chronos.control</w>
-      <w>chull</w>
-      <w>chunk</w>
-      <w>chunk.default</w>
-      <w>chunkToLineReader</w>
-      <w>chunk_dim</w>
-      <w>ci1.geneSymbol.LENGTH</w>
-      <w>ci1.refGene.LENGTH</w>
-      <w>ci1.xenoRefGene.LENGTH</w>
-      <w>ci2.ensGene.LENGTH</w>
-      <w>ci2.geneSymbol.LENGTH</w>
-      <w>ci2.refGene.LENGTH</w>
-      <w>ci2.xenoRefGene.LENGTH</w>
-      <w>ci2d</w>
-      <w>ciapower</w>
-      <w>cigar</w>
-      <w>cigarNarrow</w>
-      <w>cigarOpTable</w>
-      <w>cigarQNarrow</w>
-      <w>cigarRangesAlongPairwiseSpace</w>
-      <w>cigarRangesAlongQuerySpace</w>
-      <w>cigarRangesAlongReferenceSpace</w>
-      <w>cigarToRleList</w>
-      <w>cigarWidthAlongPairwiseSpace</w>
-      <w>cigarWidthAlongQuerySpace</w>
-      <w>cigarWidthAlongReferenceSpace</w>
-      <w>cilleruelo</w>
-      <w>cipoisson</w>
-      <w>circ.sim</w>
-      <w>circ.sim.plot</w>
-      <w>circ.simulation</w>
-      <w>circ.tests</w>
-      <w>circadian.F</w>
-      <w>circadian.cor</w>
-      <w>circadian.linear.cor</w>
-      <w>circadian.mean</w>
-      <w>circadian.phase</w>
-      <w>circadian.reliability</w>
-      <w>circadian.sd</w>
-      <w>circadian.stats</w>
-      <w>circle.layout</w>
-      <w>circleGrob</w>
-      <w>circleLayout</w>
-      <w>circlize_dendrogram</w>
-      <w>circulant</w>
-      <w>circulant.spam</w>
-      <w>circular.averaging</w>
-      <w>circular.cor</w>
-      <w>circular.mean</w>
-      <w>circular.plot</w>
-      <w>circularRandomizeRegions</w>
-      <w>citEntry</w>
-      <w>citFooter</w>
-      <w>citHeader</w>
-      <w>cit_cit_types</w>
-      <w>cit_types</w>
-      <w>citation</w>
-      <w>cite</w>
-      <w>citeNatbib</w>
-      <w>citecmd</w>
-      <w>cited.type.game</w>
-      <w>cities</w>
-      <w>citing.cited.type.game</w>
-      <w>city</w>
-      <w>cividis</w>
-      <w>cjd</w>
-      <w>cksum</w>
-      <w>clPairs</w>
-      <w>clPairsLegend</w>
-      <w>cl_agreement</w>
-      <w>cl_bag</w>
-      <w>cl_boot</w>
-      <w>cl_class_ids</w>
-      <w>cl_classes</w>
-      <w>cl_consensus</w>
-      <w>cl_dissimilarity</w>
-      <w>cl_ensemble</w>
-      <w>cl_fuzziness</w>
-      <w>cl_join</w>
-      <w>cl_margin</w>
-      <w>cl_medoid</w>
-      <w>cl_meet</w>
-      <w>cl_membership</w>
-      <w>cl_object_names</w>
-      <w>cl_pam</w>
-      <w>cl_pclust</w>
-      <w>cl_predict</w>
-      <w>cl_prototypes</w>
-      <w>cl_tabulate</w>
-      <w>cl_ultrametric</w>
-      <w>cl_validity</w>
-      <w>cladewise</w>
-      <w>cladogram.plot</w>
-      <w>clamp</w>
-      <w>clara</w>
-      <w>claraCBI</w>
-      <w>claridge</w>
-      <w>class</w>
-      <w>class.ind</w>
-      <w>class2ind</w>
-      <w>classAgreement</w>
-      <w>classDist</w>
-      <w>classError</w>
-      <w>classLabel</w>
-      <w>classMetaName</w>
-      <w>className</w>
-      <w>classNameForDisplay</w>
-      <w>classPC</w>
-      <w>classVersion</w>
-      <w>classesToAM</w>
-      <w>classifdist</w>
-      <w>classifnp</w>
-      <w>classifyTestsF</w>
-      <w>classifyTestsP</w>
-      <w>classifyTestsT</w>
-      <w>claw54</w>
-      <w>cldem</w>
-      <w>clean</w>
-      <w>clean.args</w>
-      <w>clean_cache</w>
-      <w>clean_dll</w>
-      <w>clean_site</w>
-      <w>clean_theme</w>
-      <w>clean_vignettes</w>
-      <w>cleancdfname</w>
-      <w>cleanup</w>
-      <w>cleanup.FileProgressBar</w>
-      <w>cleanup.import</w>
-      <w>cleanupBigWigCache</w>
-      <w>clearCache</w>
-      <w>clearCache.Object</w>
-      <w>clearLookupCache</w>
-      <w>clearLookupCache.Object</w>
-      <w>clearNode</w>
-      <w>clearPushBack</w>
-      <w>clearRepository</w>
-      <w>clearSearch</w>
-      <w>clearSessionCache</w>
-      <w>clearValues</w>
-      <w>clear_clip</w>
-      <w>cli</w>
-      <w>cli_sitrep</w>
-      <w>click</w>
-      <w>clickOpts</w>
-      <w>click_rotate</w>
-      <w>clip</w>
-      <w>clipGrob</w>
-      <w>clipString</w>
-      <w>clipboard</w>
-      <w>clipr</w>
-      <w>clipr_available</w>
-      <w>clique.number</w>
-      <w>clique_num</w>
-      <w>cliques</w>
-      <w>clisymbols</w>
-      <w>clock24.plot</w>
-      <w>clogit</w>
-      <w>clone</w>
-      <w>clone.Object</w>
-      <w>clone.default</w>
-      <w>clone.list</w>
-      <w>close</w>
-      <w>close.BamFile</w>
-      <w>close.BcfFile</w>
-      <w>close.FaFile</w>
-      <w>close.RsamtoolsFileList</w>
-      <w>close.ShortReadFile</w>
-      <w>close.TabixFile</w>
-      <w>close.connection</w>
-      <w>close.screen</w>
-      <w>close.socket</w>
-      <w>close.srcfile</w>
-      <w>close.srcfilealias</w>
-      <w>closeAllConnections</w>
-      <w>closeHtmlPage</w>
-      <w>closeNode</w>
-      <w>closeNode.NWSnode</w>
-      <w>closeNode.SOCKnode</w>
-      <w>closeNode.default</w>
-      <w>closePage</w>
-      <w>close_intervals</w>
-      <w>closed</w>
-      <w>closed.testing</w>
-      <w>closeness</w>
-      <w>closeness.estimate</w>
-      <w>closepb</w>
-      <w>cloth</w>
-      <w>cloud</w>
-      <w>clowess</w>
-      <w>clplot</w>
-      <w>cltest</w>
-      <w>cltrain</w>
-      <w>clucols</w>
-      <w>clue</w>
-      <w>clugrey</w>
-      <w>clujaccard</w>
-      <w>clump</w>
-      <w>clus2norMix</w>
-      <w>clusGap</w>
-      <w>clusexpect</w>
-      <w>clusplot</w>
-      <w>cluspop.nb</w>
-      <w>clustCombi</w>
-      <w>clustCombiOptim</w>
-      <w>clustal</w>
-      <w>clustalomega</w>
-      <w>clustatsum</w>
-      <w>cluster</w>
-      <w>cluster.cor</w>
-      <w>cluster.distribution</w>
-      <w>cluster.fit</w>
-      <w>cluster.loadings</w>
-      <w>cluster.magazine</w>
-      <w>cluster.overplot</w>
-      <w>cluster.plot</w>
-      <w>cluster.stats</w>
-      <w>cluster.varstats</w>
-      <w>cluster2keys</w>
-      <w>clusterApply</w>
-      <w>clusterApplyLB</w>
-      <w>clusterCTSS</w>
-      <w>clusterCall</w>
-      <w>clusterData</w>
-      <w>clusterEvalQ</w>
-      <w>clusterExport</w>
-      <w>clusterFDR</w>
-      <w>clusterMaker</w>
-      <w>clusterMap</w>
-      <w>clusterOn</w>
-      <w>clusterR</w>
-      <w>clusterRun</w>
-      <w>clusterSamples</w>
-      <w>clusterSetRNGStream</w>
-      <w>clusterSetupRNG</w>
-      <w>clusterSetupRNGstream</w>
-      <w>clusterSetupSPRNG</w>
-      <w>clusterSim</w>
-      <w>clusterSplit</w>
-      <w>clusterWindows</w>
-      <w>cluster_edge_betweenness</w>
-      <w>cluster_fast_greedy</w>
-      <w>cluster_infomap</w>
-      <w>cluster_label_prop</w>
-      <w>cluster_leading_eigen</w>
-      <w>cluster_louvain</w>
-      <w>cluster_optimal</w>
-      <w>cluster_results_table</w>
-      <w>cluster_spinglass</w>
-      <w>cluster_walktrap</w>
-      <w>clusterbenchstats</w>
-      <w>clusterboot</w>
-      <w>clustered.dotplots</w>
-      <w>clusteringCoef</w>
-      <w>clusteringCoefAppr</w>
-      <w>clusteringCoefficient</w>
-      <w>clusters</w>
-      <w>clusters.bclust</w>
-      <w>clusym</w>
-      <w>cm</w>
-      <w>cm.colors</w>
-      <w>cmahal</w>
-      <w>cmdArg</w>
-      <w>cmdArgs</w>
-      <w>cmdArgsCall</w>
-      <w>cmdscale</w>
-      <w>cmeans</w>
-      <w>cmpfile</w>
-      <w>cmpfun</w>
-      <w>cmsg</w>
-      <w>cneFinalListDanRer10Hg38</w>
-      <w>cneMerge</w>
-      <w>cnetplot</w>
-      <w>cnvrt.coords</w>
-      <w>co.intervals</w>
-      <w>co.transfer</w>
-      <w>co2</w>
-      <w>coRankedMatrices</w>
-      <w>coal</w>
-      <w>coalesce</w>
-      <w>coalescent.intervals</w>
-      <w>cobyla</w>
-      <w>cochranq.test</w>
-      <w>cocitation</w>
-      <w>coda</w>
-      <w>coda.options</w>
-      <w>codamenu</w>
-      <w>code</w>
-      <w>code.length</w>
-      <w>code.levels</w>
-      <w>code2n</w>
-      <w>code_len</w>
-      <w>codetools</w>
-      <w>codoc</w>
-      <w>codocClasses</w>
-      <w>codocData</w>
-      <w>codons</w>
-      <w>coef</w>
-      <w>coef.Krig</w>
-      <w>coef.crq</w>
-      <w>coef.hclust</w>
-      <w>coef.lars</w>
-      <w>coef.mselm</w>
-      <w>coef.nlrq</w>
-      <w>coef.selm</w>
-      <w>coef.slm</w>
-      <w>coefHier</w>
-      <w>coefci</w>
-      <w>coefci.default</w>
-      <w>coeffRV</w>
-      <w>coefficients</w>
-      <w>coefmat</w>
-      <w>coefplot</w>
-      <w>coeftest</w>
-      <w>coeftest.default</w>
-      <w>coerce</w>
-      <w>coerceValue</w>
-      <w>cohen.d</w>
-      <w>cohen.d.by</w>
-      <w>cohen.d.ci</w>
-      <w>cohen.kappa</w>
-      <w>cohesion</w>
-      <w>cohesive.blocks</w>
-      <w>cohesive_blocks</w>
-      <w>col</w>
-      <w>col.dist</w>
-      <w>col.whitebg</w>
-      <w>col01scale</w>
-      <w>col2hcl</w>
-      <w>col2hex</w>
-      <w>col2rgb</w>
-      <w>colAUC</w>
-      <w>colAlls</w>
-      <w>colAnyMissings</w>
-      <w>colAnyNAs</w>
-      <w>colAnys</w>
-      <w>colAvgsPerRowSet</w>
-      <w>colClasses</w>
-      <w>colClasses.default</w>
-      <w>colCollapse</w>
-      <w>colCounts</w>
-      <w>colCummaxs</w>
-      <w>colCummins</w>
-      <w>colCumprods</w>
-      <w>colCumsums</w>
-      <w>colData</w>
-      <w>colDiffs</w>
-      <w>colFromCell</w>
-      <w>colFromX</w>
-      <w>colFtests</w>
-      <w>colIQRDiffs</w>
-      <w>colIQRs</w>
-      <w>colLogSumExps</w>
-      <w>colMadDiffs</w>
-      <w>colMads</w>
-      <w>colMaxs</w>
-      <w>colMeans</w>
-      <w>colMeans.dist</w>
-      <w>colMeans.spam</w>
-      <w>colMeans2</w>
-      <w>colMedians</w>
-      <w>colMins</w>
-      <w>colOrderStats</w>
-      <w>colProds</w>
-      <w>colQuantiles</w>
-      <w>colRanges</w>
-      <w>colRanks</w>
-      <w>colReorder</w>
-      <w>colSdDiffs</w>
-      <w>colSds</w>
-      <w>colSummarizeAvg</w>
-      <w>colSummarizeAvgLog</w>
-      <w>colSummarizeBiweight</w>
-      <w>colSummarizeBiweightLog</w>
-      <w>colSummarizeLogAvg</w>
-      <w>colSummarizeLogMedian</w>
-      <w>colSummarizeMedian</w>
-      <w>colSummarizeMedianLog</w>
-      <w>colSummarizeMedianpolish</w>
-      <w>colSummarizeMedianpolishLog</w>
-      <w>colSums</w>
-      <w>colSums.dist</w>
-      <w>colSums.spam</w>
-      <w>colSums2</w>
-      <w>colTabulates</w>
-      <w>colVarDiffs</w>
-      <w>colVars</w>
-      <w>colWeightedMads</w>
-      <w>colWeightedMeans</w>
-      <w>colWeightedMedians</w>
-      <w>colWeightedSds</w>
-      <w>colWeightedVars</w>
-      <w>col_align</w>
-      <w>col_bin</w>
-      <w>col_black</w>
-      <w>col_blue</w>
-      <w>col_character</w>
-      <w>col_cyan</w>
-      <w>col_date</w>
-      <w>col_datetime</w>
-      <w>col_double</w>
-      <w>col_factor</w>
-      <w>col_green</w>
-      <w>col_grey</w>
-      <w>col_guess</w>
-      <w>col_integer</w>
-      <w>col_logical</w>
-      <w>col_magenta</w>
-      <w>col_means</w>
-      <w>col_nchar</w>
-      <w>col_norms</w>
-      <w>col_number</w>
-      <w>col_numeric</w>
-      <w>col_quantile</w>
-      <w>col_red</w>
-      <w>col_silver</w>
-      <w>col_skip</w>
-      <w>col_strsplit</w>
-      <w>col_substr</w>
-      <w>col_substring</w>
-      <w>col_sums</w>
-      <w>col_time</w>
-      <w>col_white</w>
-      <w>col_yellow</w>
-      <w>colapply_simple_triplet_matrix</w>
-      <w>colcenter</w>
-      <w>coleman</w>
-      <w>coll</w>
-      <w>collapse</w>
-      <w>collapse.replicates</w>
-      <w>collapse.singles</w>
-      <w>collapseBSseq</w>
-      <w>collapseReplicates</w>
-      <w>collapse_branch</w>
-      <w>collapsed.intervals</w>
-      <w>collapsef</w>
-      <w>collect</w>
-      <w>collectLocals</w>
-      <w>collectUsage</w>
-      <w>collectionType</w>
-      <w>colmask</w>
-      <w>colmetanames</w>
-      <w>colnames</w>
-      <w>colnames_style</w>
-      <w>colon</w>
-      <w>colonnade</w>
-      <w>color</w>
-      <w>color.axis</w>
-      <w>color.gradient</w>
-      <w>color.id</w>
-      <w>color.legend</w>
-      <w>color.pathway.by.objects</w>
-      <w>color.scale</w>
-      <w>color.scale.lines</w>
-      <w>color2D.matplot</w>
-      <w>colorBiasSummary</w>
-      <w>colorBlindSafePal</w>
-      <w>colorConverter</w>
-      <w>colorFacet</w>
-      <w>colorRamp</w>
-      <w>colorRampPalette</w>
-      <w>color_branches</w>
-      <w>color_labels</w>
-      <w>color_palette</w>
-      <w>color_unique_labels</w>
-      <w>colorbar</w>
-      <w>colorbar.plot</w>
-      <w>colored_bars</w>
-      <w>colored_dots</w>
-      <w>coloring</w>
-      <w>colorlegend</w>
-      <w>colorpanel</w>
-      <w>colors</w>
-      <w>colorschemes</w>
-      <w>colorspace</w>
-      <w>colorspaces</w>
-      <w>colortable</w>
-      <w>colourInput</w>
-      <w>colourPicker</w>
-      <w>colour_branches</w>
-      <w>colour_ramp</w>
-      <w>colours</w>
-      <w>cols</w>
-      <w>cols_condense</w>
-      <w>cols_only</w>
-      <w>colsel</w>
-      <w>colsplit</w>
-      <w>colttests</w>
-      <w>columb</w>
-      <w>columb.polys</w>
-      <w>column</w>
-      <w>columnMatrix</w>
-      <w>columnMetadata</w>
-      <w>column_glossary</w>
-      <w>column_to_rownames</w>
-      <w>columns</w>
-      <w>colwise</w>
-      <w>combMat</w>
-      <w>combiPlot</w>
-      <w>combiTree</w>
-      <w>combinat</w>
-      <w>combinations</w>
-      <w>combine</w>
-      <w>combine.levels</w>
-      <w>combine27k450k</w>
-      <w>combineArrays</w>
-      <w>combineLabels</w>
-      <w>combineLimits</w>
-      <w>combineList</w>
-      <w>combineNodes</w>
-      <w>combineOverlaps</w>
-      <w>combineResults</w>
-      <w>combineScores</w>
-      <w>combineTests</w>
-      <w>combineVar</w>
-      <w>combineVarReports</w>
-      <w>combine_ansi_styles</w>
-      <w>combine_styles</w>
-      <w>combine_vars</w>
-      <w>combine_words</w>
-      <w>combinedControlPlot</w>
-      <w>combn</w>
-      <w>combn2</w>
-      <w>combo</w>
-      <w>combos</w>
-      <w>combs</w>
-      <w>comma</w>
-      <w>comma_format</w>
-      <w>commandArgs</w>
-      <w>comment</w>
-      <w>comment.SAX</w>
-      <w>commit</w>
-      <w>commits</w>
-      <w>commonCondLogLikDerDelta</w>
-      <w>commonName</w>
-      <w>commonRegions</w>
-      <w>common_by</w>
-      <w>common_env</w>
-      <w>common_subtrees_clusters</w>
-      <w>communities</w>
-      <w>commutation</w>
-      <w>comorbidity</w>
-      <w>comp.test</w>
-      <w>compCDF</w>
-      <w>compCorrGraph</w>
-      <w>compGdist</w>
-      <w>compact</w>
-      <w>compactPDF</w>
-      <w>compactToMat</w>
-      <w>compactToMatC</w>
-      <w>compactVignettes</w>
-      <w>compar.cheverud</w>
-      <w>compar.gee</w>
-      <w>compar.lynch</w>
-      <w>compar.ou</w>
-      <w>compare</w>
-      <w>compare.matrix</w>
-      <w>compareCRS</w>
-      <w>compareCoefs</w>
-      <w>compareFactors</w>
-      <w>compareFits</w>
-      <w>compareGrowthCurves</w>
-      <w>compareMatchedClasses</w>
-      <w>compareModels</w>
-      <w>comparePhylo</w>
-      <w>comparePred</w>
-      <w>compareRaster</w>
-      <w>compareStrings</w>
-      <w>compareTwoGrowthCurves</w>
-      <w>compareVersion</w>
-      <w>compareXMLDocs</w>
-      <w>compare_Rcheck</w>
-      <w>compare_checks</w>
-      <w>compare_distributions</w>
-      <w>compare_means</w>
-      <w>compare_models</w>
-      <w>compare_tbls</w>
-      <w>compare_tbls2</w>
-      <w>compare_to_cran</w>
-      <w>compare_usage1</w>
-      <w>compartments</w>
-      <w>compassRose</w>
-      <w>compatibleGenomes</w>
-      <w>compatibleVersions</w>
-      <w>compclassf.classify</w>
-      <w>compclassf.train</w>
-      <w>compile</w>
-      <w>compile.Rdoc</w>
-      <w>compile.SmartComments</w>
-      <w>compileAttributes</w>
-      <w>compilePKGS</w>
-      <w>compileRdoc</w>
-      <w>compile_dll</w>
-      <w>compile_src</w>
-      <w>compiler</w>
-      <w>compiler_flags</w>
-      <w>complement</w>
-      <w>complement_slice</w>
-      <w>complementer</w>
-      <w>complete</w>
-      <w>complete.cases</w>
-      <w>completeClassDefinition</w>
-      <w>completeExtends</w>
-      <w>completeSubclasses</w>
-      <w>complete_</w>
-      <w>complex</w>
-      <w>complexitylevels</w>
-      <w>complik</w>
-      <w>compnames</w>
-      <w>component_distribution</w>
-      <w>component_wise</w>
-      <w>components</w>
-      <w>compose</w>
-      <w>compresid2way</w>
-      <w>compressBeadData</w>
-      <w>compressFile</w>
-      <w>compressFile.default</w>
-      <w>compressPDF</w>
-      <w>compressPDF.default</w>
-      <w>compute</w>
-      <w>compute.brlen</w>
-      <w>compute.brtime</w>
-      <w>computeAllFlinks</w>
-      <w>computeExprSet</w>
-      <w>computeGeneSetsOverlap</w>
-      <w>computeMode</w>
-      <w>computeRestarts</w>
-      <w>computeSpikeFactors</w>
-      <w>computeSumFactors</w>
-      <w>con.comp</w>
-      <w>con.regmat</w>
-      <w>con2cat</w>
-      <w>con2tr</w>
-      <w>conTestkw</w>
-      <w>concatHtmlTables</w>
-      <w>concatenateMatrices</w>
-      <w>concordance</w>
-      <w>concordancefit</w>
-      <w>concurvity</w>
-      <w>condLogLikDerDelta</w>
-      <w>condLogLikDerSize</w>
-      <w>condense</w>
-      <w>condentropy</w>
-      <w>condes</w>
-      <w>condest</w>
-      <w>condinformation</w>
-      <w>condition</w>
-      <w>conditionCall</w>
-      <w>conditionCall.condition</w>
-      <w>conditionMessage</w>
-      <w>conditionMessage.condition</w>
-      <w>conditionStackTrace</w>
-      <w>conditional</w>
-      <w>conditionalFormat</w>
-      <w>conditionalFormatting</w>
-      <w>conditionalPanel</w>
-      <w>conditionalSECdistr</w>
-      <w>conditions</w>
-      <w>condroz</w>
-      <w>conexp</w>
-      <w>confInt</w>
-      <w>confband</w>
-      <w>confbar</w>
-      <w>confidence.ellipse</w>
-      <w>confidenceEllipse</w>
-      <w>config</w>
-      <w>confint</w>
-      <w>confint.default</w>
-      <w>confint.lm</w>
-      <w>confint.segmented</w>
-      <w>confint.selm</w>
-      <w>confint_tidy</w>
-      <w>conflicts</w>
-      <w>conformMethod</w>
-      <w>confpred</w>
-      <w>confusion</w>
-      <w>confusion.matrix</w>
-      <w>confusionMatrix</w>
-      <w>confusionMatrix.train</w>
-      <w>congeneric.sim</w>
-      <w>conlnorm</w>
-      <w>connComp</w>
-      <w>conn_create_fd</w>
-      <w>conn_create_file</w>
-      <w>conn_create_pipepair</w>
-      <w>conn_disable_inheritance</w>
-      <w>conn_get_fileno</w>
-      <w>conn_is_incomplete</w>
-      <w>conn_read_chars</w>
-      <w>conn_read_lines</w>
-      <w>conn_set_stderr</w>
-      <w>conn_set_stdout</w>
-      <w>conn_write</w>
-      <w>connect</w>
-      <w>connect.neighborhood</w>
-      <w>connectedComp</w>
-      <w>conpl</w>
-      <w>consensus</w>
-      <w>consensusClusters</w>
-      <w>consensusClustersTpm</w>
-      <w>consensusMatrix</w>
-      <w>consensusString</w>
-      <w>consensusViews</w>
-      <w>consensus_matrix</w>
-      <w>consensus_tree</w>
-      <w>console</w>
-      <w>console_width</w>
-      <w>consolidate</w>
-      <w>consolidateClusters</w>
-      <w>consolidateSizes</w>
-      <w>consolidateTrack</w>
-      <w>constantFold</w>
-      <w>constrOptim</w>
-      <w>constrain</w>
-      <w>constrain_pars</w>
-      <w>constraint</w>
-      <w>constraints</w>
-      <w>constructCVSTModel</w>
-      <w>constructData</w>
-      <w>constructFastKRRLearner</w>
-      <w>constructKRRLearner</w>
-      <w>constructKlogRegLearner</w>
-      <w>constructLearner</w>
-      <w>constructParams</w>
-      <w>constructSVMLearner</w>
-      <w>constructSVRLearner</w>
-      <w>constructSequentialTest</w>
-      <w>contTable</w>
-      <w>containLetters</w>
-      <w>contains</w>
-      <w>content</w>
-      <w>content_type</w>
-      <w>content_type_json</w>
-      <w>content_type_xml</w>
-      <w>contents</w>
-      <w>continuous_scale</w>
-      <w>contour</w>
-      <w>contour.default</w>
-      <w>contourLines</w>
-      <w>contourplot</w>
-      <w>contr</w>
-      <w>contr.Helmert</w>
-      <w>contr.SAS</w>
-      <w>contr.Sum</w>
-      <w>contr.Treatment</w>
-      <w>contr.dummy</w>
-      <w>contr.helmert</w>
-      <w>contr.ltfr</w>
-      <w>contr.poly</w>
-      <w>contr.sdif</w>
-      <w>contr.sum</w>
-      <w>contr.treatment</w>
-      <w>contract</w>
-      <w>contract.vertices</w>
-      <w>contrastAsCoef</w>
-      <w>contrasts</w>
-      <w>contrasts.fit</w>
-      <w>contrasts.varFit</w>
-      <w>contrib.url</w>
-      <w>contributions</w>
-      <w>contributor</w>
-      <w>contributors</w>
-      <w>control</w>
-      <w>control.errorest</w>
-      <w>controlClusterFDR</w>
-      <w>controlCode</w>
-      <w>controlData</w>
-      <w>controlProbeDetection</w>
-      <w>controlStatus</w>
-      <w>controlStripPlot</w>
-      <w>controlTypes</w>
-      <w>controlled_geneset_enrichment</w>
-      <w>convergence</w>
-      <w>convert</w>
-      <w>convert.group.labels</w>
-      <w>convertArray</w>
-      <w>convertBeadLevelList</w>
-      <w>convertColor</w>
-      <w>convertColsToList</w>
-      <w>convertComment</w>
-      <w>convertComment.SmartComments</w>
-      <w>convertComment.VComments</w>
-      <w>convertDataFrameCols</w>
-      <w>convertDfCols</w>
-      <w>convertFilter</w>
-      <w>convertFromExcelRef</w>
-      <w>convertHeight</w>
-      <w>convertInteger</w>
-      <w>convertIntegers</w>
-      <w>convertListOfRowsToDataFrame</w>
-      <w>convertMatrixType</w>
-      <w>convertNative</w>
-      <w>convertRowsToList</w>
-      <w>convertTheme</w>
-      <w>convertTo</w>
-      <w>convertToDate</w>
-      <w>convertToDateTime</w>
-      <w>convertToShortString</w>
-      <w>convertUnit</w>
-      <w>convertWidth</w>
-      <w>convertX</w>
-      <w>convertY</w>
-      <w>convest</w>
-      <w>convex.hull</w>
-      <w>convex_hull</w>
-      <w>convhulln</w>
-      <w>convolve</w>
-      <w>conweibull</w>
-      <w>cookd</w>
-      <w>cookies</w>
-      <w>cooks.distance</w>
-      <w>coolmap</w>
-      <w>coop</w>
-      <w>coord.ellipse</w>
-      <w>coord2dist</w>
-      <w>coordProj</w>
-      <w>coord_cartesian</w>
-      <w>coord_equal</w>
-      <w>coord_fixed</w>
-      <w>coord_flip</w>
-      <w>coord_map</w>
-      <w>coord_munch</w>
-      <w>coord_polar</w>
-      <w>coord_quickmap</w>
-      <w>coord_sf</w>
-      <w>coord_trans</w>
-      <w>coordinates</w>
-      <w>coordinatevalues</w>
-      <w>coordnames</w>
-      <w>coords</w>
-      <w>cophenetic</w>
-      <w>cophenetic.phylo</w>
-      <w>cophenetic_correlation</w>
-      <w>cophyloplot</w>
-      <w>coplot</w>
-      <w>copy</w>
-      <w>copyDependencyToDir</w>
-      <w>copyDirectory</w>
-      <w>copyDirectory.default</w>
-      <w>copyEnv</w>
-      <w>copyFile</w>
-      <w>copyFile.default</w>
-      <w>copyRequiredJobFiles</w>
-      <w>copySubstitute</w>
-      <w>copyWorkbook</w>
-      <w>copy_tinytex</w>
-      <w>copy_to</w>
-      <w>cor</w>
-      <w>cor.ci</w>
-      <w>cor.dendlist</w>
-      <w>cor.fk</w>
-      <w>cor.mtest</w>
-      <w>cor.na</w>
-      <w>cor.plot</w>
-      <w>cor.plot.upperLowerCi</w>
-      <w>cor.smooth</w>
-      <w>cor.smoother</w>
-      <w>cor.test</w>
-      <w>cor.wt</w>
-      <w>cor2</w>
-      <w>cor2cov</w>
-      <w>cor2dist</w>
-      <w>cor2latex</w>
-      <w>corAR1</w>
-      <w>corARMA</w>
-      <w>corBlomberg</w>
-      <w>corBrownian</w>
-      <w>corCAR1</w>
-      <w>corCi</w>
-      <w>corCompSymm</w>
-      <w>corExp</w>
-      <w>corFactor</w>
-      <w>corFiml</w>
-      <w>corGaus</w>
-      <w>corGrafen</w>
-      <w>corIdent</w>
-      <w>corLin</w>
-      <w>corLocal</w>
-      <w>corMartins</w>
-      <w>corMatrix</w>
-      <w>corNatural</w>
-      <w>corPagel</w>
-      <w>corPlot</w>
-      <w>corPlotUpperLowerCi</w>
-      <w>corRatio</w>
-      <w>corSpatial</w>
-      <w>corSpher</w>
-      <w>corSymm</w>
-      <w>cor_FM_index</w>
-      <w>cor_bakers_gamma</w>
-      <w>cor_common_nodes</w>
-      <w>cor_cophenetic</w>
-      <w>coredata</w>
-      <w>coredata.default</w>
-      <w>coreness</w>
-      <w>cores</w>
-      <w>coriell</w>
-      <w>corner.label</w>
-      <w>corphylo</w>
-      <w>corplot</w>
-      <w>corr</w>
-      <w>corr.Tn</w>
-      <w>corr.null</w>
-      <w>corr.p</w>
-      <w>corr.test</w>
-      <w>corrMatOrder</w>
-      <w>corrRect</w>
-      <w>corrRect.hclust</w>
-      <w>correct</w>
-      <w>correct.cor</w>
-      <w>correctI</w>
-      <w>correctII</w>
-      <w>correct_counts</w>
-      <w>correlateNull</w>
-      <w>correlatePairs</w>
-      <w>correlateReads</w>
-      <w>correlation</w>
-      <w>correlogram</w>
-      <w>correlogram.formula</w>
-      <w>corresp</w>
-      <w>corrplot</w>
-      <w>corrplot.mixed</w>
-      <w>cortest</w>
-      <w>cortest.bartlett</w>
-      <w>cortest.jennrich</w>
-      <w>cortest.mat</w>
-      <w>cortest.normal</w>
-      <w>cortex_mrna</w>
-      <w>cos</w>
-      <w>cosh</w>
-      <w>cosinor</w>
-      <w>cosinor.period</w>
-      <w>cosinor.plot</w>
-      <w>cospi</w>
-      <w>couldBeLonLat</w>
-      <w>count</w>
-      <w>count.fields</w>
-      <w>count.links</w>
-      <w>count.mappedLkeys</w>
-      <w>count.mappedRkeys</w>
-      <w>count.mappedkeys</w>
-      <w>count.multiple</w>
-      <w>count.overplot</w>
-      <w>count.pairwise</w>
-      <w>countBam</w>
-      <w>countBipartitions</w>
-      <w>countCompatibleOverlaps</w>
-      <w>countDumpedAlignments</w>
-      <w>countFa</w>
-      <w>countGenesInTerm</w>
-      <w>countLines</w>
-      <w>countLines.default</w>
-      <w>countLnodeHits</w>
-      <w>countMatches</w>
-      <w>countOverlaps</w>
-      <w>countPDict</w>
-      <w>countPWM</w>
-      <w>countPaths</w>
-      <w>countPattern</w>
-      <w>countQueryHits</w>
-      <w>countRangeset</w>
-      <w>countRnodeHits</w>
-      <w>countSubjectHits</w>
-      <w>countTabix</w>
-      <w>count_</w>
-      <w>count_components</w>
-      <w>count_fields</w>
-      <w>count_isomorphisms</w>
-      <w>count_max_cliques</w>
-      <w>count_motifs</w>
-      <w>count_multiple</w>
-      <w>count_subgraph_isomorphisms</w>
-      <w>count_terminal_nodes</w>
-      <w>count_triangles</w>
-      <w>counties</w>
-      <w>countpattern</w>
-      <w>counts</w>
-      <w>county.fips</w>
-      <w>countyMapEnv</w>
-      <w>couple</w>
-      <w>cout</w>
-      <w>cov</w>
-      <w>cov.exp</w>
-      <w>cov.mat</w>
-      <w>cov.mcd</w>
-      <w>cov.mve</w>
-      <w>cov.nug</w>
-      <w>cov.rob</w>
-      <w>cov.sph</w>
-      <w>cov.trob</w>
-      <w>cov.wend1</w>
-      <w>cov.wend2</w>
-      <w>cov.wml</w>
-      <w>cov.wt</w>
-      <w>cov.wu1</w>
-      <w>cov.wu2</w>
-      <w>cov.wu3</w>
-      <w>cov2cor</w>
-      <w>covComed</w>
-      <w>covGK</w>
-      <w>covMcd</w>
-      <w>covMest</w>
-      <w>covOGK</w>
-      <w>covPC</w>
-      <w>covPCAgrid</w>
-      <w>covPCAproj</w>
-      <w>covPlot</w>
-      <w>covariance</w>
-      <w>covariate_type</w>
-      <w>covariates</w>
-      <w>cover</w>
-      <w>cover.design</w>
-      <w>coverage</w>
-      <w>coverageByTranscript</w>
-      <w>coverageGR</w>
-      <w>covers</w>
-      <w>covfix</w>
-      <w>covmat</w>
-      <w>covplot</w>
-      <w>covratio</w>
-      <w>covw</w>
-      <w>cowplot</w>
-      <w>cox.ph</w>
-      <w>cox.zph</w>
-      <w>coxExponential.lvm</w>
-      <w>coxGompertz.lvm</w>
-      <w>coxWeibull.lvm</w>
-      <w>coxY</w>
-      <w>coxfilter</w>
-      <w>coxph</w>
-      <w>coxph.control</w>
-      <w>coxph.detail</w>
-      <w>coxph.fit</w>
-      <w>coxph.wtest</w>
-      <w>coxtest</w>
-      <w>cp</w>
-      <w>cp2dp</w>
-      <w>cpar</w>
-      <w>cpg.annotate</w>
-      <w>cpgCollapse</w>
-      <w>cpgIslands</w>
-      <w>cpgram</w>
-      <w>cpm</w>
-      <w>cpm.DGEList</w>
-      <w>cpm.default</w>
-      <w>cpmByGroup</w>
-      <w>cpmByGroup.DGEList</w>
-      <w>cpmByGroup.default</w>
-      <w>cpneTrack</w>
-      <w>cpower</w>
-      <w>cppFunction</w>
-      <w>cpp_object_dummy</w>
-      <w>cpp_object_initializer</w>
-      <w>cpplot</w>
-      <w>cppls</w>
-      <w>cprint</w>
-      <w>cprintf</w>
-      <w>cpus</w>
-      <w>cqcluster.stats</w>
-      <w>cr.plot</w>
-      <w>cr.plots</w>
-      <w>crModel</w>
-      <w>crPlot</w>
-      <w>crPlots</w>
-      <w>crabB_MvsF</w>
-      <w>crabF_BvsO</w>
-      <w>crabM_BvsO</w>
-      <w>crabO_MvsF</w>
-      <w>crab_BvsO</w>
-      <w>crab_MvsF</w>
-      <w>crabs</w>
-      <w>cran_ascii_fields</w>
-      <w>cran_check_flavours</w>
-      <w>cran_check_results</w>
-      <w>cran_valid_fields</w>
-      <w>crayon</w>
-      <w>crc1.GeRL</w>
-      <w>create</w>
-      <w>create.communities</w>
-      <w>create.post</w>
-      <w>createAnnObjs.SchemaChoice</w>
-      <w>createComment</w>
-      <w>createCorMatrix</w>
-      <w>createDataPartition</w>
-      <w>createFileAtomically</w>
-      <w>createFileAtomically.default</w>
-      <w>createFolds</w>
-      <w>createFunctionsList</w>
-      <w>createGEOMatrix</w>
-      <w>createGEOMeta</w>
-      <w>createLLChrCats</w>
-      <w>createLink</w>
-      <w>createLink.default</w>
-      <w>createMAPIncMat</w>
-      <w>createMOFAobject</w>
-      <w>createManPath</w>
-      <w>createManPath.Rdoc</w>
-      <w>createModel</w>
-      <w>createMultiFolds</w>
-      <w>createName</w>
-      <w>createName.Rdoc</w>
-      <w>createNamedRegion</w>
-      <w>createPackage</w>
-      <w>createProjectTemplate</w>
-      <w>createRandomRegions</w>
-      <w>createRenderFunction</w>
-      <w>createResample</w>
-      <w>createSimpleBimap</w>
-      <w>createStyle</w>
-      <w>createTargetsFile</w>
-      <w>createTimeSlices</w>
-      <w>createWebDependency</w>
-      <w>createWidget</w>
-      <w>createWindowsShortcut</w>
-      <w>createWindowsShortcut.default</w>
-      <w>createWorkbook</w>
-      <w>create_description</w>
-      <w>create_env</w>
-      <w>create_from_github</w>
-      <w>create_gene_covar_file</w>
-      <w>create_package</w>
-      <w>create_progress_bar</w>
-      <w>create_project</w>
-      <w>create_tidy_package</w>
-      <w>create_traceback</w>
-      <w>creationDate</w>
-      <w>cred_env</w>
-      <w>cred_ssh_key</w>
-      <w>cred_token</w>
-      <w>cred_user_pass</w>
-      <w>credit_data</w>
-      <w>crepuscule</w>
-      <w>cricket_CvsP</w>
-      <w>crimtab</w>
-      <w>crit</w>
-      <w>criteria</w>
-      <w>critval</w>
-      <w>crmatrix</w>
-      <w>crop</w>
-      <w>crop.image</w>
-      <w>cross</w>
-      <w>cross2</w>
-      <w>cross3</w>
-      <w>crossCoVGram</w>
-      <w>cross_d</w>
-      <w>cross_df</w>
-      <w>cross_n</w>
-      <w>crossapply_simple_triplet_matrix</w>
-      <w>crosscorr</w>
-      <w>crosscorr.plot</w>
-      <w>crossentropy</w>
-      <w>crossing</w>
-      <w>crossing_</w>
-      <w>crossprod</w>
-      <w>crossprod.spam</w>
-      <w>crossprod_simple_triplet_matrix</w>
-      <w>crosstab</w>
-      <w>crosstalk</w>
-      <w>crosstalkLibs</w>
-      <w>crossval</w>
-      <w>crp</w>
-      <w>crplot</w>
-      <w>crq</w>
-      <w>crq.fit.pen</w>
-      <w>crq.fit.por</w>
-      <w>crq.fit.por2</w>
-      <w>crq.fit.pow</w>
-      <w>crs</w>
-      <w>crs2lm</w>
-      <w>crul</w>
-      <w>crul_settings</w>
-      <w>crunch</w>
-      <w>cs</w>
-      <w>csaw</w>
-      <w>csawUsersGuide</w>
-      <w>cscale</w>
-      <w>cshell</w>
-      <w>cshow</w>
-      <w>csi</w>
-      <w>csplit</w>
-      <w>csrf</w>
-      <w>css</w>
-      <w>cstr</w>
-      <w>csv.get</w>
-      <w>cta</w>
-      <w>cta.15</w>
-      <w>ctapply</w>
-      <w>ctd</w>
-      <w>ctlcurves</w>
-      <w>ctreeBag</w>
-      <w>cu.summary</w>
-      <w>cube</w>
-      <w>cube2</w>
-      <w>cubic.cov</w>
-      <w>cubits</w>
-      <w>cum.Vert.funkt</w>
-      <w>cum3</w>
-      <w>cumOverlap</w>
-      <w>cumall</w>
-      <w>cumany</w>
-      <w>cumcategory</w>
-      <w>cume_dist</w>
-      <w>cummax</w>
-      <w>cummean</w>
-      <w>cummin</w>
-      <w>cumprod</w>
-      <w>cumsum</w>
-      <w>cumsumexact</w>
-      <w>cumulant.digamma</w>
-      <w>cumulativeCTSSdistribution</w>
-      <w>cumuplot</w>
-      <w>curl</w>
-      <w>curlError</w>
-      <w>curlEscape</w>
-      <w>curlGetHeaders</w>
-      <w>curlGlobalInit</w>
-      <w>curlMultiPerform</w>
-      <w>curlOptions</w>
-      <w>curlPercentEncode</w>
-      <w>curlPerform</w>
-      <w>curlSetOpt</w>
-      <w>curlUnescape</w>
-      <w>curlVersion</w>
-      <w>curl_docs</w>
-      <w>curl_download</w>
-      <w>curl_echo</w>
-      <w>curl_escape</w>
-      <w>curl_fds</w>
-      <w>curl_fetch_disk</w>
-      <w>curl_fetch_echo</w>
-      <w>curl_fetch_memory</w>
-      <w>curl_fetch_multi</w>
-      <w>curl_fetch_stream</w>
-      <w>curl_options</w>
-      <w>curl_symbols</w>
-      <w>curl_unescape</w>
-      <w>curl_version</w>
-      <w>curly</w>
-      <w>currencysubstitution</w>
-      <w>current.column</w>
-      <w>current.panel.limits</w>
-      <w>current.parent</w>
-      <w>current.rotation</w>
-      <w>current.row</w>
-      <w>current.transform</w>
-      <w>current.viewport</w>
-      <w>current.vpPath</w>
-      <w>current.vpTree</w>
-      <w>currentTimeMillis</w>
-      <w>currentTimeMillis.System</w>
-      <w>current_info</w>
-      <w>current_input</w>
-      <w>current_vars</w>
-      <w>curve</w>
-      <w>curveGrob</w>
-      <w>curveRep</w>
-      <w>curveSmooth</w>
-      <w>curve_multiple</w>
-      <w>cushny</w>
-      <w>custom.theme</w>
-      <w>custom.theme.2</w>
-      <w>cut</w>
-      <w>cut.Date</w>
-      <w>cut.POSIXt</w>
-      <w>cut.default</w>
-      <w>cut2</w>
-      <w>cutOff</w>
-      <w>cutWithMinN</w>
-      <w>cut_at</w>
-      <w>cut_interval</w>
-      <w>cut_lower_fun</w>
-      <w>cut_number</w>
-      <w>cut_width</w>
-      <w>cutat</w>
-      <w>cuthill.mckee.ordering</w>
-      <w>cutree</w>
-      <w>cutreeDynamic</w>
-      <w>cutreeDynamicTree</w>
-      <w>cutreeHybrid</w>
-      <w>cutree_1h.dendrogram</w>
-      <w>cutree_1k.dendrogram</w>
-      <w>cv</w>
-      <w>cv.MclustDA</w>
-      <w>cv.folds</w>
-      <w>cv.glm</w>
-      <w>cv.lars</w>
-      <w>cv1EMtrain</w>
-      <w>cvMclustDA</w>
-      <w>cvd_emulator</w>
-      <w>cvnn</w>
-      <w>cvsegments</w>
-      <w>cweight</w>
-      <w>cxxfunction</w>
-      <w>cy3</w>
-      <w>cy5</w>
-      <w>cyan</w>
-      <w>cycle</w>
-      <w>cyclical_scale</w>
-      <w>cyclone</w>
-      <w>cylindrect</w>
-      <w>cynipids</w>
-      <w>cyp2b10</w>
-      <w>cytoBand</w>
-      <w>d.ci</w>
-      <w>d.robust</w>
-      <w>d.stat</w>
-      <w>d2cumulant.digamma</w>
-      <w>d2r</w>
-      <w>d2sigmoid</w>
-      <w>d2t</w>
-      <w>dChip.colors</w>
-      <w>dDA</w>
-      <w>dDeta</w>
-      <w>dFNCHypergeo</w>
-      <w>dMFNCHypergeo</w>
-      <w>dMWNCHypergeo</w>
-      <w>dQuote</w>
-      <w>dSymmModulated</w>
-      <w>dWNCHypergeo</w>
-      <w>d_ply</w>
-      <w>dag.sp</w>
-      <w>daisy</w>
-      <w>dalton</w>
-      <w>danRer3.ensGene.LENGTH</w>
-      <w>danRer3.geneSymbol.LENGTH</w>
-      <w>danRer3.refGene.LENGTH</w>
-      <w>danRer4.ensGene.LENGTH</w>
-      <w>danRer4.geneSymbol.LENGTH</w>
-      <w>danRer4.genscan.LENGTH</w>
-      <w>danRer4.nscanGene.LENGTH</w>
-      <w>danRer4.refGene.LENGTH</w>
-      <w>danRer5.ensGene.LENGTH</w>
-      <w>danRer5.geneSymbol.LENGTH</w>
-      <w>danRer5.refGene.LENGTH</w>
-      <w>danRer5.vegaGene.LENGTH</w>
-      <w>danRer5.vegaPseudoGene.LENGTH</w>
-      <w>danRer6.ensGene.LENGTH</w>
-      <w>danRer6.geneSymbol.LENGTH</w>
-      <w>danRer6.refGene.LENGTH</w>
-      <w>danRer6.xenoRefGene.LENGTH</w>
-      <w>dandelion.plot</w>
-      <w>danen</w>
-      <w>danes</w>
-      <w>danet</w>
-      <w>danishmulti</w>
-      <w>danishuni</w>
-      <w>daply</w>
-      <w>dapply</w>
-      <w>darken</w>
-      <w>darker</w>
-      <w>darned_hg19_subset500</w>
-      <w>darwin</w>
-      <w>dasen</w>
-      <w>dashboardBody</w>
-      <w>dashboardHeader</w>
-      <w>dashboardPage</w>
-      <w>dashboardSidebar</w>
-      <w>dat</w>
-      <w>data</w>
-      <w>data.Zou</w>
-      <w>data.class</w>
-      <w>data.ellipse</w>
-      <w>data.entry</w>
-      <w>data.frame</w>
-      <w>data.frame2GRanges</w>
-      <w>data.matrix</w>
-      <w>data.restore</w>
-      <w>data.table</w>
-      <w>dataDensityString</w>
-      <w>dataDetectPval2NA</w>
-      <w>dataEllipse</w>
-      <w>dataFAQlog1</w>
-      <w>dataFAQscale1</w>
-      <w>dataFAQscale2</w>
-      <w>dataFrame</w>
-      <w>dataFrame.default</w>
-      <w>dataPath</w>
-      <w>dataRep</w>
-      <w>dataSetList</w>
-      <w>dataSigned</w>
-      <w>dataSize</w>
-      <w>dataSource</w>
-      <w>dataTable</w>
-      <w>dataTableAjax</w>
-      <w>dataTableOutput</w>
-      <w>dataTableProxy</w>
-      <w>dataType</w>
-      <w>dataURI</w>
-      <w>dataValidation</w>
-      <w>dataViewport</w>
-      <w>data_frame</w>
-      <w>data_frame_</w>
-      <w>database</w>
-      <w>datadensity</w>
-      <w>dataentry</w>
-      <w>dataf</w>
-      <w>dataf.geneexp</w>
-      <w>dataf.growth</w>
-      <w>dataf.medflies</w>
-      <w>dataf.population</w>
-      <w>dataf.population2010</w>
-      <w>dataf.sim.1.CFF07</w>
-      <w>dataf.sim.2.CFF07</w>
-      <w>dataf.tecator</w>
-      <w>dataf2rawfd</w>
-      <w>dataframe2asc</w>
-      <w>dataframeReduce</w>
-      <w>datasets</w>
-      <w>datasetsDb</w>
-      <w>datasource</w>
-      <w>datatable</w>
-      <w>date</w>
-      <w>dateInput</w>
-      <w>dateRangeInput</w>
-      <w>date_breaks</w>
-      <w>date_decimal</w>
-      <w>date_format</w>
-      <w>date_names</w>
-      <w>date_names_lang</w>
-      <w>date_names_langs</w>
-      <w>date_trans</w>
-      <w>daten1</w>
-      <w>daten2</w>
-      <w>davies.test</w>
-      <w>day</w>
-      <w>dayOfWeek</w>
-      <w>dayOfYear</w>
-      <w>days</w>
-      <w>days_in_month</w>
-      <w>db1</w>
-      <w>dbAppendTable</w>
-      <w>dbApply</w>
-      <w>dbBegin</w>
-      <w>dbBeginTransaction</w>
-      <w>dbBind</w>
-      <w>dbBreak</w>
-      <w>dbBuildTableDefinition</w>
-      <w>dbCallProc</w>
-      <w>dbCanConnect</w>
-      <w>dbClearResult</w>
-      <w>dbColumnInfo</w>
-      <w>dbCommit</w>
-      <w>dbConnect</w>
-      <w>dbCreateJobDefTable</w>
-      <w>dbCreateTable</w>
-      <w>dbDataType</w>
-      <w>dbDisconnect</w>
-      <w>dbDriver</w>
-      <w>dbEscapeStrings</w>
-      <w>dbExecute</w>
-      <w>dbExistsTable</w>
-      <w>dbFetch</w>
-      <w>dbFileConnect</w>
-      <w>dbFileDisconnect</w>
-      <w>dbGetDBIVersion</w>
-      <w>dbGetException</w>
-      <w>dbGetInfo</w>
-      <w>dbGetJobs</w>
-      <w>dbGetPreparedQuery</w>
-      <w>dbGetQuery</w>
-      <w>dbGetRowCount</w>
-      <w>dbGetRowsAffected</w>
-      <w>dbGetStatement</w>
-      <w>dbGetTable</w>
-      <w>dbHasCompleted</w>
-      <w>dbInfo</w>
-      <w>dbIsReadOnly</w>
-      <w>dbIsValid</w>
-      <w>dbListConnections</w>
-      <w>dbListFields</w>
-      <w>dbListObjects</w>
-      <w>dbListResults</w>
-      <w>dbListTables</w>
-      <w>dbMoreResults</w>
-      <w>dbNextResult</w>
-      <w>dbQuoteIdentifier</w>
-      <w>dbQuoteLiteral</w>
-      <w>dbQuoteString</w>
-      <w>dbReadTable</w>
-      <w>dbRemoveTable</w>
-      <w>dbRollback</w>
-      <w>dbSendPreparedQuery</w>
-      <w>dbSendQuery</w>
-      <w>dbSendStatement</w>
-      <w>dbSetDataMappings</w>
-      <w>dbUnloadDriver</w>
-      <w>dbUnquoteIdentifier</w>
-      <w>dbWithTransaction</w>
-      <w>dbWriteTable</w>
-      <w>db_analyze</w>
-      <w>db_begin</w>
-      <w>db_commit</w>
-      <w>db_create_index</w>
-      <w>db_create_indexes</w>
-      <w>db_create_table</w>
-      <w>db_data_type</w>
-      <w>db_desc</w>
-      <w>db_drop_table</w>
-      <w>db_explain</w>
-      <w>db_has_table</w>
-      <w>db_insert_into</w>
-      <w>db_list_tables</w>
-      <w>db_query_fields</w>
-      <w>db_query_rows</w>
-      <w>db_rollback</w>
-      <w>db_save_query</w>
-      <w>db_write_table</w>
-      <w>dbconn</w>
-      <w>dbd</w>
-      <w>dbdTime</w>
-      <w>dbeta</w>
-      <w>dbfile</w>
-      <w>dbinom</w>
-      <w>dbiwt</w>
-      <w>dblclickOpts</w>
-      <w>dbmeta</w>
-      <w>dbscan</w>
-      <w>dbscanCBI</w>
-      <w>dbschema</w>
-      <w>dbvalog</w>
-      <w>dbvamix</w>
-      <w>dbvaneglog</w>
-      <w>dbvbilog</w>
-      <w>dbvct</w>
-      <w>dbvevd</w>
-      <w>dbvhr</w>
-      <w>dbvlog</w>
-      <w>dbvnegbilog</w>
-      <w>dbvneglog</w>
-      <w>dcast</w>
-      <w>dcast.data.table</w>
-      <w>dcauchy</w>
-      <w>dchisq</w>
-      <w>dcor0</w>
-      <w>dd2dms</w>
-      <w>ddalpha</w>
-      <w>ddalpha.classify</w>
-      <w>ddalpha.getErrorRateCV</w>
-      <w>ddalpha.getErrorRatePart</w>
-      <w>ddalpha.test</w>
-      <w>ddalpha.train</w>
-      <w>ddalphaf.classify</w>
-      <w>ddalphaf.getErrorRateCV</w>
-      <w>ddalphaf.getErrorRatePart</w>
-      <w>ddalphaf.test</w>
-      <w>ddalphaf.train</w>
-      <w>ddays</w>
-      <w>ddf_Lb</w>
-      <w>ddfind</w>
-      <w>ddirichlet</w>
-      <w>ddiscrete</w>
-      <w>ddmmmyy</w>
-      <w>ddply</w>
-      <w>de</w>
-      <w>de.ncols</w>
-      <w>de.restore</w>
-      <w>de.setup</w>
-      <w>de_bruijn_graph</w>
-      <w>death_reg</w>
-      <w>deaths</w>
-      <w>debounce</w>
-      <w>debug</w>
-      <w>debug.affy123</w>
-      <w>debug.lr</w>
-      <w>debugGatherer</w>
-      <w>debugMulticore</w>
-      <w>debugSQL</w>
-      <w>debugSSH</w>
-      <w>debug_fseq</w>
-      <w>debug_pipe</w>
-      <w>debugcall</w>
-      <w>debugger</w>
-      <w>debuggingState</w>
-      <w>debugonce</w>
-      <w>decapitalize</w>
-      <w>decapitalize.default</w>
-      <w>decathlon</w>
-      <w>decathlon2</w>
-      <w>decide.special.case</w>
-      <w>decideTests</w>
-      <w>decideTests.DGEExact</w>
-      <w>decideTests.DGELRT</w>
-      <w>decideTests.MArrayLM</w>
-      <w>decideTests.default</w>
-      <w>decideTestsDGE</w>
-      <w>decimal_date</w>
-      <w>declaration</w>
-      <w>declaration.Rdoc</w>
-      <w>decode</w>
-      <w>decodeURI</w>
-      <w>decodeURIComponent</w>
-      <w>decomp.specials</w>
-      <w>decomp2sigma</w>
-      <w>decompose</w>
-      <w>decompose.graph</w>
-      <w>decomposeVar</w>
-      <w>decompressBeadData</w>
-      <w>decompressFile</w>
-      <w>decompressFile.default</w>
-      <w>decrypt_envelope</w>
-      <w>def</w>
-      <w>default.DNAcopy.bdry</w>
-      <w>default.stringsAsFactors</w>
-      <w>defaultClusterOptions</w>
-      <w>defaultDumpName</w>
-      <w>defaultPrior</w>
-      <w>defaultPrototype</w>
-      <w>defaultSummary</w>
-      <w>default_locale</w>
-      <w>default_output_format</w>
-      <w>default_repos</w>
-      <w>default_signature</w>
-      <w>default_site_generator</w>
-      <w>defaults</w>
-      <w>defer</w>
-      <w>defer_parent</w>
-      <w>deff</w>
-      <w>defineTestSuite</w>
-      <w>defmacro</w>
-      <w>deframe</w>
-      <w>degAxis</w>
-      <w>degree</w>
-      <w>degree.distribution</w>
-      <w>degree.sequence.game</w>
-      <w>degreeLabelsEW</w>
-      <w>degreeLabelsNS</w>
-      <w>degree_distribution</w>
-      <w>degseq</w>
-      <w>del.colgapsonly</w>
-      <w>del.gaps</w>
-      <w>del.rowgapsonly</w>
-      <w>delaunayn</w>
-      <w>delay</w>
-      <w>delayedAssign</w>
-      <w>delcol</w>
-      <w>delete.edges</w>
-      <w>delete.response</w>
-      <w>delete.vertices</w>
-      <w>deleteData</w>
-      <w>delete_edge_attr</w>
-      <w>delete_edges</w>
-      <w>delete_graph_attr</w>
-      <w>delete_vertex_attr</w>
-      <w>delete_vertices</w>
-      <w>deletion</w>
-      <w>delimMatch</w>
-      <w>delivery</w>
-      <w>delta.plot</w>
-      <w>deltaMethod</w>
-      <w>deltat</w>
-      <w>demangle</w>
-      <w>demo</w>
-      <w>demo_spinners</w>
-      <w>demoplot</w>
-      <w>dendPlot</w>
-      <w>dend_diff</w>
-      <w>dend_expend</w>
-      <w>dendbackback</w>
-      <w>dendextend</w>
-      <w>dendextend_options</w>
-      <w>dendlist</w>
-      <w>dendrapply</w>
-      <w>dendroPlot</w>
-      <w>dendrogramGrob</w>
-      <w>denoisePCA</w>
-      <w>denom_vars</w>
-      <w>dens</w>
-      <w>dens.est</w>
-      <w>densCols</w>
-      <w>denscomp</w>
-      <w>denseAnnTrack</w>
-      <w>dense_rank</w>
-      <w>density</w>
-      <w>density.default</w>
-      <w>density.lf</w>
-      <w>density.npEM</w>
-      <w>density.sim</w>
-      <w>density.spEM</w>
-      <w>densityBeanPlot</w>
-      <w>densityBy</w>
-      <w>densityByProbeType</w>
-      <w>densityMclust</w>
-      <w>densityMclust.diagnostic</w>
-      <w>densityPlot</w>
-      <w>densityplot</w>
-      <w>densplot</w>
-      <w>denspr</w>
-      <w>denuh</w>
-      <w>denumerate</w>
-      <w>dep_auto</w>
-      <w>dep_prev</w>
-      <w>dep_types</w>
-      <w>depan</w>
-      <w>deparse</w>
-      <w>deparseLatex</w>
-      <w>deparse_usage</w>
-      <w>deparse_usage1</w>
-      <w>dependsOnPkgs</w>
-      <w>depth</w>
-      <w>depth.</w>
-      <w>depth.L2</w>
-      <w>depth.Mahalanobis</w>
-      <w>depth.betaSkeleton</w>
-      <w>depth.contours</w>
-      <w>depth.contours.ddalpha</w>
-      <w>depth.graph</w>
-      <w>depth.halfspace</w>
-      <w>depth.potential</w>
-      <w>depth.projection</w>
-      <w>depth.qhpeeling</w>
-      <w>depth.sample</w>
-      <w>depth.simplicial</w>
-      <w>depth.simplicialVolume</w>
-      <w>depth.space.</w>
-      <w>depth.space.Mahalanobis</w>
-      <w>depth.space.halfspace</w>
-      <w>depth.space.potential</w>
-      <w>depth.space.projection</w>
-      <w>depth.space.simplicial</w>
-      <w>depth.space.simplicialVolume</w>
-      <w>depth.space.spatial</w>
-      <w>depth.space.zonoid</w>
-      <w>depth.spatial</w>
-      <w>depth.zonoid</w>
-      <w>depthf.</w>
-      <w>depthf.ABD</w>
-      <w>depthf.BD</w>
-      <w>depthf.HR</w>
-      <w>depthf.RP1</w>
-      <w>depthf.RP2</w>
-      <w>depthf.fd1</w>
-      <w>depthf.fd2</w>
-      <w>depthf.hM</w>
-      <w>depthf.hM2</w>
-      <w>deratify</w>
-      <w>deriv</w>
-      <w>deriv3</w>
-      <w>derivatives.est</w>
-      <w>derive</w>
-      <w>desaturate</w>
-      <w>desc</w>
-      <w>desc_add_author</w>
-      <w>desc_add_me</w>
-      <w>desc_add_remotes</w>
-      <w>desc_add_role</w>
-      <w>desc_add_to_collate</w>
-      <w>desc_add_urls</w>
-      <w>desc_bump_version</w>
-      <w>desc_change_maintainer</w>
-      <w>desc_clear_remotes</w>
-      <w>desc_clear_urls</w>
-      <w>desc_del</w>
-      <w>desc_del_author</w>
-      <w>desc_del_collate</w>
-      <w>desc_del_dep</w>
-      <w>desc_del_deps</w>
-      <w>desc_del_from_collate</w>
-      <w>desc_del_remotes</w>
-      <w>desc_del_role</w>
-      <w>desc_del_urls</w>
-      <w>desc_fields</w>
-      <w>desc_get</w>
-      <w>desc_get_author</w>
-      <w>desc_get_authors</w>
-      <w>desc_get_built</w>
-      <w>desc_get_collate</w>
-      <w>desc_get_deps</w>
-      <w>desc_get_field</w>
-      <w>desc_get_maintainer</w>
-      <w>desc_get_or_fail</w>
-      <w>desc_get_remotes</w>
-      <w>desc_get_urls</w>
-      <w>desc_get_version</w>
-      <w>desc_has_dep</w>
-      <w>desc_has_fields</w>
-      <w>desc_normalize</w>
-      <w>desc_print</w>
-      <w>desc_reformat_fields</w>
-      <w>desc_reorder_fields</w>
-      <w>desc_set</w>
-      <w>desc_set_authors</w>
-      <w>desc_set_collate</w>
-      <w>desc_set_dep</w>
-      <w>desc_set_deps</w>
-      <w>desc_set_remotes</w>
-      <w>desc_set_urls</w>
-      <w>desc_set_version</w>
-      <w>desc_statby</w>
-      <w>desc_to_latex</w>
-      <w>desc_validate</w>
-      <w>descdist</w>
-      <w>descendant_of</w>
-      <w>descendants</w>
-      <w>descentDetails</w>
-      <w>descfreq</w>
-      <w>describe</w>
-      <w>describe.by</w>
-      <w>describeBy</w>
-      <w>describeData</w>
-      <w>describeFast</w>
-      <w>describecoef</w>
-      <w>description</w>
-      <w>design</w>
-      <w>design.matrix</w>
-      <w>designAsFactor</w>
-      <w>designI2A</w>
-      <w>designI2M</w>
-      <w>designIItoMandU</w>
-      <w>designIItoMandU2</w>
-      <w>designItoMandU</w>
-      <w>designItoMandU2</w>
-      <w>designer.colors</w>
-      <w>destination</w>
-      <w>destructure</w>
-      <w>det</w>
-      <w>detach</w>
-      <w>detach.BasicObject</w>
-      <w>detach.Object</w>
-      <w>detach.default</w>
-      <w>detachPackage</w>
-      <w>detachPackage.default</w>
-      <w>detail</w>
-      <w>detailRanges</w>
-      <w>details</w>
-      <w>detect</w>
-      <w>detectCores</w>
-      <w>detectOutlier</w>
-      <w>detect_index</w>
-      <w>detect_step</w>
-      <w>detectbound</w>
-      <w>detection</w>
-      <w>detectionCall</w>
-      <w>detectionP</w>
-      <w>detectionPValues</w>
-      <w>detectionPValues.EListRaw</w>
-      <w>detectionPValues.default</w>
-      <w>detectionPval.filter</w>
-      <w>determinant</w>
-      <w>determinant.matrix</w>
-      <w>determinant.spam</w>
-      <w>determinant.spam.chol.NgPeyton</w>
-      <w>deutan</w>
-      <w>deutanomaly_cvd</w>
-      <w>dev.capabilities</w>
-      <w>dev.capture</w>
-      <w>dev.control</w>
-      <w>dev.copy</w>
-      <w>dev.copy2eps</w>
-      <w>dev.copy2pdf</w>
-      <w>dev.cur</w>
-      <w>dev.flush</w>
-      <w>dev.hold</w>
-      <w>dev.interactive</w>
-      <w>dev.list</w>
-      <w>dev.new</w>
-      <w>dev.next</w>
-      <w>dev.off</w>
-      <w>dev.prev</w>
-      <w>dev.print</w>
-      <w>dev.set</w>
-      <w>dev.size</w>
-      <w>dev2bitmap</w>
-      <w>devAskNewPage</w>
-      <w>dev_example</w>
-      <w>dev_help</w>
-      <w>dev_meta</w>
-      <w>dev_mode</w>
-      <w>dev_package_deps</w>
-      <w>dev_packages</w>
-      <w>dev_topic_index_reset</w>
-      <w>devcoords</w>
-      <w>deviance</w>
-      <w>deviance.RefFreeCellMix</w>
-      <w>deviance.ace</w>
-      <w>deviance.nlrq</w>
-      <w>deviance.slm</w>
-      <w>deviceIsInteractive</w>
-      <w>devtest</w>
-      <w>devtools</w>
-      <w>dexp</w>
-      <w>dextreme</w>
-      <w>df</w>
-      <w>df.kernel</w>
-      <w>df.residual</w>
-      <w>df2latex</w>
-      <w>dfOrder</w>
-      <w>dfbeta</w>
-      <w>dfbetaPlots</w>
-      <w>dfbetas</w>
-      <w>dfbetasPlots</w>
-      <w>dffits</w>
-      <w>dfort</w>
-      <w>dfrechet</w>
-      <w>dfs</w>
-      <w>dfs2</w>
-      <w>dfsfit</w>
-      <w>dgamma</w>
-      <w>dgebal</w>
-      <w>dgeom</w>
-      <w>dget</w>
-      <w>dgev</w>
-      <w>dglmStdResid</w>
-      <w>dgpd</w>
-      <w>dgumbel</w>
-      <w>dhalfnorm</w>
-      <w>dhfr</w>
-      <w>dhistboxp</w>
-      <w>dhours</w>
-      <w>dhyper</w>
-      <w>di2multi</w>
-      <w>di2multi.multiPhylo</w>
-      <w>di2multi.phylo</w>
-      <w>dia.arrow</w>
-      <w>dia.cone</w>
-      <w>dia.curve</w>
-      <w>dia.curved.arrow</w>
-      <w>dia.ellipse</w>
-      <w>dia.ellipse1</w>
-      <w>dia.rect</w>
-      <w>dia.self</w>
-      <w>dia.shape</w>
-      <w>dia.triangle</w>
-      <w>diab</w>
-      <w>diabetes</w>
-      <w>diabetic</w>
-      <w>diag</w>
-      <w>diag.of.spam</w>
-      <w>diag.off</w>
-      <w>diag.panel.splom</w>
-      <w>diag.spam</w>
-      <w>diagDA</w>
-      <w>diagN2U</w>
-      <w>diagU2N</w>
-      <w>diagX</w>
-      <w>diagnostics</w>
-      <w>diagram</w>
-      <w>diagresidues</w>
-      <w>diagtest</w>
-      <w>dialogViewer</w>
-      <w>diameter</w>
-      <w>diamondplot</w>
-      <w>diamonds</w>
-      <w>diana</w>
-      <w>dicedist</w>
-      <w>dichromat</w>
-      <w>dichromat.pal.blind.info</w>
-      <w>dichromat_pal</w>
-      <w>dictionariesPath</w>
-      <w>diff</w>
-      <w>diff.AtomicList</w>
-      <w>diff.Date</w>
-      <w>diff.POSIXt</w>
-      <w>diff.Rle</w>
-      <w>diff.default</w>
-      <w>diff.difftime</w>
-      <w>diff.spam</w>
-      <w>diff2</w>
-      <w>diffSplice</w>
-      <w>diffSpliceDGE</w>
-      <w>diff_express</w>
-      <w>difference</w>
-      <w>differential_splicing</w>
-      <w>diffinv</w>
-      <w>diffmeanX</w>
-      <w>diffs.1.N</w>
-      <w>difftime</w>
-      <w>difftimeDate</w>
-      <w>diffuse</w>
-      <w>diffusionKmeans</w>
-      <w>diffusionMap</w>
-      <w>digamma</w>
-      <w>digest</w>
-      <w>digest2int</w>
-      <w>digits</w>
-      <w>digits2number</w>
-      <w>digitsBase</w>
-      <w>dijkstra.sp</w>
-      <w>dim</w>
-      <w>dim.CompressedMatrix</w>
-      <w>dim.DGEExact</w>
-      <w>dim.DGEGLM</w>
-      <w>dim.DGELRT</w>
-      <w>dim.DGEList</w>
-      <w>dim.EList</w>
-      <w>dim.EListRaw</w>
-      <w>dim.MAList</w>
-      <w>dim.MArrayLM</w>
-      <w>dim.RGList</w>
-      <w>dim.TopTags</w>
-      <w>dim.data.frame</w>
-      <w>dimColor</w>
-      <w>dimLabels</w>
-      <w>dimRed</w>
-      <w>dimRedData</w>
-      <w>dimRedMethodList</w>
-      <w>dimRedQualityList</w>
-      <w>dimRedResult</w>
-      <w>dim_desc</w>
-      <w>dim_select</w>
-      <w>dimdesc</w>
-      <w>dimension</w>
-      <w>dimension.default</w>
-      <w>dimensions</w>
-      <w>dimnames</w>
-      <w>dimnames.DGEExact</w>
-      <w>dimnames.DGEGLM</w>
-      <w>dimnames.DGELRT</w>
-      <w>dimnames.DGEList</w>
-      <w>dimnames.EList</w>
-      <w>dimnames.EListRaw</w>
-      <w>dimnames.MAList</w>
-      <w>dimnames.MArrayLM</w>
-      <w>dimnames.RGList</w>
-      <w>dimnames.TopTags</w>
-      <w>dimnames.data.frame</w>
-      <w>dims</w>
-      <w>dinucleotideFrequency</w>
-      <w>dinucleotideFrequencyTest</w>
-      <w>dinvgamma</w>
-      <w>dinvgauss</w>
-      <w>dip</w>
-      <w>dip.test</w>
-      <w>dipp.tantrum</w>
-      <w>diptest</w>
-      <w>diptest.multi</w>
-      <w>dir</w>
-      <w>dir.create</w>
-      <w>dir.exists</w>
-      <w>dir_copy</w>
-      <w>dir_create</w>
-      <w>dir_delete</w>
-      <w>dir_exists</w>
-      <w>dir_info</w>
-      <w>dir_ls</w>
-      <w>dir_map</w>
-      <w>dir_tree</w>
-      <w>dir_walk</w>
-      <w>direct</w>
-      <w>directL</w>
-      <w>directSl</w>
-      <w>directed_graph</w>
-      <w>direction</w>
-      <w>dirichlet_multinomial_anova</w>
-      <w>dirichlet_multinomial_anova_mc</w>
-      <w>dirichlet_multinomial_glm</w>
-      <w>dirname</w>
-      <w>disable</w>
-      <w>disabled</w>
-      <w>disaggregate</w>
-      <w>disassemble</w>
-      <w>discard</w>
-      <w>discover_repository</w>
-      <w>discoveries</w>
-      <w>discr_coords</w>
-      <w>discrcoord</w>
-      <w>discrete</w>
-      <w>discrete.recode</w>
-      <w>discrete_scale</w>
-      <w>discretize</w>
-      <w>discretize.image</w>
-      <w>discrproj</w>
-      <w>disexp</w>
-      <w>disjoin</w>
-      <w>disjointBins</w>
-      <w>disjointExons</w>
-      <w>disjoint_union</w>
-      <w>diskCache</w>
-      <w>dislnorm</w>
-      <w>dispBinTrend</w>
-      <w>dispCoxReid</w>
-      <w>dispCoxReidInterpolateTagwise</w>
-      <w>dispCoxReidPowerTrend</w>
-      <w>dispCoxReidSplineTrend</w>
-      <w>dispDeviance</w>
-      <w>dispPearson</w>
-      <w>dispTable</w>
-      <w>dispersion</w>
-      <w>dispersionFunction</w>
-      <w>dispersions</w>
-      <w>displ</w>
-      <w>display</w>
-      <w>display.brewer.all</w>
-      <w>display.brewer.pal</w>
-      <w>display.coda.options</w>
-      <w>display.spam</w>
-      <w>displayCode</w>
-      <w>displayCode.default</w>
-      <w>displayPars</w>
-      <w>dispois</w>
-      <w>dist</w>
-      <w>dist.aa</w>
-      <w>dist.dendlist</w>
-      <w>dist.dna</w>
-      <w>dist.gene</w>
-      <w>dist.nodes</w>
-      <w>dist.topo</w>
-      <w>dist2</w>
-      <w>dist_all_cdf</w>
-      <w>dist_cdf</w>
-      <w>dist_data_all_cdf</w>
-      <w>dist_data_cdf</w>
-      <w>dist_ll</w>
-      <w>dist_long</w>
-      <w>dist_pdf</w>
-      <w>dist_rand</w>
-      <w>distance</w>
-      <w>distanceFromPoints</w>
-      <w>distanceToNearest</w>
-      <w>distance_correlation</w>
-      <w>distance_table</w>
-      <w>distance_to_nearest</w>
-      <w>distancefactor</w>
-      <w>distances</w>
-      <w>distcritmulti</w>
-      <w>disthclustCBI</w>
-      <w>disthclusttreeCBI</w>
-      <w>distinct</w>
-      <w>distinct_</w>
-      <w>distinct_edges</w>
-      <w>distmesh2d</w>
-      <w>distmeshnd</w>
-      <w>distnoisemclustCBI</w>
-      <w>distortionMin</w>
-      <w>distratio</w>
-      <w>distributeNegation</w>
-      <w>distribution</w>
-      <w>distrsimilarity</w>
-      <w>dither</w>
-      <w>div</w>
-      <w>div_gradient_pal</w>
-      <w>diverge_hcl</w>
-      <w>diverge_hsv</w>
-      <w>divergex_hcl</w>
-      <w>diverging_hcl</w>
-      <w>diverging_hsv</w>
-      <w>diverging_pal</w>
-      <w>divergingx_hcl</w>
-      <w>divergingx_palettes</w>
-      <w>diversi.gof</w>
-      <w>diversi.time</w>
-      <w>diversity</w>
-      <w>diversity.contrast.test</w>
-      <w>divide_by</w>
-      <w>divide_by_int</w>
-      <w>diwish</w>
-      <w>djd</w>
-      <w>dknn.classify</w>
-      <w>dknn.classify.trained</w>
-      <w>dknn.train</w>
-      <w>dlnorm</w>
-      <w>dlogis</w>
-      <w>dlply</w>
-      <w>dm1.geneSymbol.LENGTH</w>
-      <w>dm1.genscan.LENGTH</w>
-      <w>dm1.refGene.LENGTH</w>
-      <w>dm2.geneSymbol.LENGTH</w>
-      <w>dm2.geneid.LENGTH</w>
-      <w>dm2.genscan.LENGTH</w>
-      <w>dm2.nscanGene.LENGTH</w>
-      <w>dm2.refGene.LENGTH</w>
-      <w>dm3.geneSymbol.LENGTH</w>
-      <w>dm3.nscanPasaGene.LENGTH</w>
-      <w>dm3.refGene.LENGTH</w>
-      <w>dmSymmModulated</w>
-      <w>dmaket</w>
-      <w>dmft</w>
-      <w>dmicroseconds</w>
-      <w>dmilliseconds</w>
-      <w>dminutes</w>
-      <w>dmnom</w>
-      <w>dmnorm</w>
-      <w>dmpFinder</w>
-      <w>dmrFinder</w>
-      <w>dmrcate</w>
-      <w>dmrcatedata</w>
-      <w>dmrse</w>
-      <w>dmrse_col</w>
-      <w>dmrse_row</w>
-      <w>dmsc</w>
-      <w>dmsn</w>
-      <w>dmst</w>
-      <w>dmt</w>
-      <w>dmultinom</w>
-      <w>dmvalog</w>
-      <w>dmvevd</w>
-      <w>dmvlog</w>
-      <w>dmvn0</w>
-      <w>dmvnorm</w>
-      <w>dmvt</w>
-      <w>dmy</w>
-      <w>dmy_h</w>
-      <w>dmy_hm</w>
-      <w>dmy_hms</w>
-      <w>dnanoseconds</w>
-      <w>dnbinom</w>
-      <w>dnds</w>
-      <w>dnoncenhypergeom</w>
-      <w>dnorMix</w>
-      <w>dnorMixL</w>
-      <w>dnorm</w>
-      <w>dnweibull</w>
-      <w>do</w>
-      <w>do.breaks</w>
-      <w>do.call</w>
-      <w>do.call2</w>
-      <w>do.index</w>
-      <w>doCall</w>
-      <w>doCall.default</w>
-      <w>doMC</w>
-      <w>doParallel</w>
-      <w>doPrimitiveMethod</w>
-      <w>doRNG</w>
-      <w>doRNGversion</w>
-      <w>doRenderTags</w>
-      <w>doSNOW</w>
-      <w>doScale</w>
-      <w>doSim</w>
-      <w>do_</w>
-      <w>do_read_bib</w>
-      <w>docName</w>
-      <w>docall</w>
-      <w>document</w>
-      <w>documentClose</w>
-      <w>documentNew</w>
-      <w>documentSave</w>
-      <w>documentSaveAll</w>
-      <w>document_position</w>
-      <w>document_range</w>
-      <w>dog_for_status</w>
-      <w>dogs</w>
-      <w>dollar</w>
-      <w>dollar_format</w>
-      <w>domain</w>
-      <w>dominator.tree</w>
-      <w>dominatorTree</w>
-      <w>dominator_tree</w>
-      <w>dontCheck</w>
-      <w>dopb</w>
-      <w>doppler</w>
-      <w>dorder</w>
-      <w>dose.p</w>
-      <w>dot</w>
-      <w>dotCall64</w>
-      <w>dotPlot</w>
-      <w>dot_product</w>
-      <w>dotbl</w>
-      <w>dotchart</w>
-      <w>dotchart2</w>
-      <w>dotchart3</w>
-      <w>dotchartp</w>
-      <w>dotchartpl</w>
-      <w>dotplot</w>
-      <w>dotplot.mtb</w>
-      <w>dotsInPolys</w>
-      <w>dots_capture</w>
-      <w>double</w>
-      <w>double.exp</w>
-      <w>doubleYScale</w>
-      <w>double_quote</w>
-      <w>down</w>
-      <w>downSample</w>
-      <w>downViewport</w>
-      <w>downdateR</w>
-      <w>download.file</w>
-      <w>download.packages</w>
-      <w>downloadButton</w>
-      <w>downloadFile</w>
-      <w>downloadFile.character</w>
-      <w>downloadGEObedFiles</w>
-      <w>downloadGSMbedFiles</w>
-      <w>downloadHandler</w>
-      <w>downloadLink</w>
-      <w>download_file</w>
-      <w>download_html</w>
-      <w>download_ssl_cert</w>
-      <w>download_users</w>
-      <w>download_version</w>
-      <w>download_xml</w>
-      <w>downs.bc</w>
-      <w>downsampleCounts</w>
-      <w>downstream</w>
-      <w>dp2.genscan.LENGTH</w>
-      <w>dp2.xenoRefGene.LENGTH</w>
-      <w>dp2cp</w>
-      <w>dp2op</w>
-      <w>dp3.geneid.LENGTH</w>
-      <w>dp3.genscan.LENGTH</w>
-      <w>dp3.xenoRefGene.LENGTH</w>
-      <w>dpicoseconds</w>
-      <w>dpih</w>
-      <w>dpik</w>
-      <w>dpill</w>
-      <w>dplcon</w>
-      <w>dpldis</w>
-      <w>dplyr</w>
-      <w>dpnorMix</w>
-      <w>dpois</w>
-      <w>dpp</w>
-      <w>dput</w>
-      <w>dr_clipr</w>
-      <w>dr_devtools</w>
-      <w>dr_dplyr</w>
-      <w>dr_github</w>
-      <w>draft</w>
-      <w>drape.color</w>
-      <w>drape.plot</w>
-      <w>draw</w>
-      <w>draw.arc</w>
-      <w>draw.circle</w>
-      <w>draw.colorkey</w>
-      <w>draw.cor</w>
-      <w>draw.ddplot</w>
-      <w>draw.density</w>
-      <w>draw.details</w>
-      <w>draw.ellipse</w>
-      <w>draw.history</w>
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-      <w>draw.pairwise.venn</w>
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-      <w>estimateGLMTagwiseDisp.default</w>
-      <w>estimateGLMTrendedDisp</w>
-      <w>estimateGLMTrendedDisp.DGEList</w>
-      <w>estimateGLMTrendedDisp.default</w>
-      <w>estimateIntensity</w>
-      <w>estimateLumiCV</w>
-      <w>estimateM</w>
-      <w>estimateMLEForBetaPriorVar</w>
-      <w>estimateMethylationBG</w>
-      <w>estimateSizeFactors</w>
-      <w>estimateSizeFactorsForMatrix</w>
-      <w>estimateTagwiseDisp</w>
-      <w>estimateTagwiseDisp.DGEList</w>
-      <w>estimateTagwiseDisp.default</w>
-      <w>estimateTrendedDisp</w>
-      <w>estimateTrendedDisp.DGEList</w>
-      <w>estimateTrendedDisp.default</w>
-      <w>estimate_betweenness</w>
-      <w>estimate_closeness</w>
-      <w>estimate_edge_betweenness</w>
-      <w>estimate_pars</w>
-      <w>estimate_xmin</w>
-      <w>estimate_yj</w>
-      <w>estimethod</w>
-      <w>ethanol</w>
-      <w>euro</w>
-      <w>eurodist</w>
-      <w>eval</w>
-      <w>eval.parent</w>
-      <w>eval.quoted</w>
-      <w>evalCapture</w>
-      <w>evalCpp</w>
-      <w>evalOnLoad</w>
-      <w>evalSeparately</w>
-      <w>evalSource</w>
-      <w>evalWithTimeout</w>
-      <w>eval_data_col</w>
-      <w>eval_fork</w>
-      <w>eval_safe</w>
-      <w>eval_tbls</w>
-      <w>eval_tbls2</w>
-      <w>evalq</w>
-      <w>evalqOnLoad</w>
-      <w>evaluate</w>
-      <w>evaluate.GString</w>
-      <w>evaluate.NullVerbose</w>
-      <w>evaluate.Verbose</w>
-      <w>evcent</w>
-      <w>evd</w>
-      <w>even</w>
-      <w>event.chart</w>
-      <w>event.convert</w>
-      <w>event.history</w>
-      <w>eventReactive</w>
-      <w>eventTime</w>
-      <w>event_data</w>
-      <w>event_register</w>
-      <w>event_unregister</w>
-      <w>every</w>
-      <w>everything</w>
-      <w>evidenceCode</w>
-      <w>evind.test</w>
-      <w>evlpoly</w>
-      <w>evlpoly2</w>
-      <w>evmc</w>
-      <w>evonet</w>
-      <w>ewLasso</w>
-      <w>ewce.plot</w>
-      <w>ewce_expression_data</w>
-      <w>eweeks</w>
-      <w>eweights</w>
-      <w>exAM</w>
-      <w>exHartigan</w>
-      <w>exactTest</w>
-      <w>exactTestBetaApprox</w>
-      <w>exactTestByDeviance</w>
-      <w>exactTestBySmallP</w>
-      <w>exactTestDoubleTail</w>
-      <w>example</w>
-      <w>example.lumi</w>
-      <w>example.lumiMethy</w>
-      <w>example.methyTitration</w>
-      <w>exampleCAGEset</w>
-      <w>exampleLevels</w>
-      <w>examplePathways</w>
-      <w>exampleRanks</w>
-      <w>example_genelist</w>
-      <w>example_loglik_array</w>
-      <w>example_loglik_matrix</w>
-      <w>excel_format</w>
-      <w>excel_sheets</w>
-      <w>exclude.too.far</w>
-      <w>excludeStaticPath</w>
-      <w>exec_background</w>
-      <w>exec_internal</w>
-      <w>exec_status</w>
-      <w>exec_wait</w>
-      <w>executeCommand</w>
-      <w>exi</w>
-      <w>exiplot</w>
-      <w>existGradient</w>
-      <w>exists</w>
-      <w>existsFunction</w>
-      <w>existsMethod</w>
-      <w>exit</w>
-      <w>exit.NullVerbose</w>
-      <w>exit.Verbose</w>
-      <w>exitCheck</w>
-      <w>exogenous</w>
-      <w>exon</w>
-      <w>exon.segment</w>
-      <w>exonicParts</w>
-      <w>exons</w>
-      <w>exonsBy</w>
-      <w>exonsByOverlaps</w>
-      <w>exp</w>
-      <w>exp.tilt</w>
-      <w>expAtv</w>
-      <w>expRMM_EM</w>
-      <w>exp_trans</w>
-      <w>expand</w>
-      <w>expand.grid</w>
-      <w>expand.model.frame</w>
-      <w>expandAsMatrix</w>
-      <w>expandParameters</w>
-      <w>expand_</w>
-      <w>expand_dots</w>
-      <w>expand_limits</w>
-      <w>expand_list</w>
-      <w>expand_range</w>
-      <w>expand_scale</w>
-      <w>expcov</w>
-      <w>expect_known_display</w>
-      <w>expectedCounts</w>
-      <w>experimentData</w>
-      <w>experimentPath</w>
-      <w>experiments</w>
-      <w>expinfo</w>
-      <w>expit</w>
-      <w>explain</w>
-      <w>explode</w>
-      <w>explodeCigarOpLengths</w>
-      <w>explodeCigarOps</w>
-      <w>explodePaths</w>
-      <w>exploreData</w>
-      <w>explvar</w>
-      <w>expm</w>
-      <w>expm.Higham08</w>
-      <w>expm1</w>
-      <w>expmCond</w>
-      <w>expmFrechet</w>
-      <w>expoTrans</w>
-      <w>export</w>
-      <w>export.2bit</w>
-      <w>export.bed</w>
-      <w>export.bed15</w>
-      <w>export.bedGraph</w>
-      <w>export.bw</w>
-      <w>export.gff</w>
-      <w>export.gff1</w>
-      <w>export.gff2</w>
-      <w>export.gff3</w>
-      <w>export.ucsc</w>
-      <w>export.wig</w>
-      <w>exportCTSStoBedGraph</w>
-      <w>exportFASTA</w>
-      <w>exportPajek</w>
-      <w>exportTestValues</w>
-      <w>exportToBed</w>
-      <w>exportToTabix</w>
-      <w>exportTracks</w>
-      <w>export_pajek</w>
-      <w>exposeClass</w>
-      <w>expose_stan_functions</w>
-      <w>expr</w>
-      <w>expr.tree</w>
-      <w>exprToFunction</w>
-      <w>expr_env</w>
-      <w>expr_find</w>
-      <w>expr_label</w>
-      <w>expr_text</w>
-      <w>express.summary.stat</w>
-      <w>express.summary.stat.methods</w>
-      <w>expression</w>
-      <w>expressionClasses</w>
-      <w>expressionMatrix</w>
-      <w>expressionQCPipeline</w>
-      <w>expressionSet133a</w>
-      <w>expression_GSE19380</w>
-      <w>expresso</w>
-      <w>expressoWidget</w>
-      <w>exprs</w>
-      <w>exprs.MA</w>
-      <w>extSoftVersion</w>
-      <w>extend</w>
-      <w>extend.BasicObject</w>
-      <w>extend.Interface</w>
-      <w>extend.Object</w>
-      <w>extend.default</w>
-      <w>extendRegions</w>
-      <w>extendShinyjs</w>
-      <w>extend_simple_sparse_array</w>
-      <w>extended</w>
-      <w>extended.figures</w>
-      <w>extended_breaks</w>
-      <w>extendrange</w>
-      <w>extends</w>
-      <w>extension</w>
-      <w>extension.diagram</w>
-      <w>extent</w>
-      <w>extentFromCells</w>
-      <w>externalRefMethod</w>
-      <w>extprod3d</w>
-      <w>extra_cols</w>
-      <w>extract</w>
-      <w>extract.array</w>
-      <w>extract.clade</w>
-      <w>extract.data</w>
-      <w>extract.default</w>
-      <w>extract.lme.cov</w>
-      <w>extract.lme.cov2</w>
-      <w>extract.matrix</w>
-      <w>extract.mixturepars</w>
-      <w>extract.popsize</w>
-      <w>extract2</w>
-      <w>extractAB</w>
-      <w>extractAIC</w>
-      <w>extractAIC.nlrq</w>
-      <w>extractAIC.rq</w>
-      <w>extractAIC.slm</w>
-      <w>extractAlignmentRangesOnReference</w>
-      <w>extractAllMatches</w>
-      <w>extractAssayDataFromList2</w>
-      <w>extractAt</w>
-      <w>extractBarcodeAndPosition</w>
-      <w>extractCoords</w>
-      <w>extractExpressionClass</w>
-      <w>extractFromTo</w>
-      <w>extractGraphAM</w>
-      <w>extractGraphBAM</w>
-      <w>extractList</w>
-      <w>extractLocalFun</w>
-      <w>extractLocsFile</w>
-      <w>extractPath</w>
-      <w>extractPrediction</w>
-      <w>extractPreserveChunks</w>
-      <w>extractProb</w>
-      <w>extractQueryStartInTranscript</w>
-      <w>extractROWS</w>
-      <w>extractRanges</w>
-      <w>extractReads</w>
-      <w>extractSECdistr</w>
-      <w>extractSeqlevels</w>
-      <w>extractSeqlevelsByGroup</w>
-      <w>extractSkippedExonRanks</w>
-      <w>extractSpannedExonRanks</w>
-      <w>extractStackTrace</w>
-      <w>extractSteppedExonRanks</w>
-      <w>extractSubList</w>
-      <w>extractTranscriptSeqs</w>
-      <w>extractUpstreamSeqs</w>
-      <w>extract_</w>
-      <w>extract_log_lik</w>
-      <w>extract_numeric</w>
-      <w>extract_raw_output</w>
-      <w>extract_sparse_parts</w>
-      <w>eyears</w>
-      <w>f.pvalue</w>
-      <w>f.robftest</w>
-      <w>f1Score</w>
-      <w>fData</w>
-      <w>fScore</w>
-      <w>f_capture</w>
-      <w>f_env</w>
-      <w>f_eval</w>
-      <w>f_eval_lhs</w>
-      <w>f_eval_rhs</w>
-      <w>f_interp</w>
-      <w>f_label</w>
-      <w>f_lhs</w>
-      <w>f_list</w>
-      <w>f_new</w>
-      <w>f_rhs</w>
-      <w>f_text</w>
-      <w>f_unwrap</w>
-      <w>fa</w>
-      <w>fa.congruence</w>
-      <w>fa.diagram</w>
-      <w>fa.extend</w>
-      <w>fa.extension</w>
-      <w>fa.graph</w>
-      <w>fa.lookup</w>
-      <w>fa.multi</w>
-      <w>fa.multi.diagram</w>
-      <w>fa.organize</w>
-      <w>fa.parallel</w>
-      <w>fa.parallel.poly</w>
-      <w>fa.plot</w>
-      <w>fa.poly</w>
-      <w>fa.random</w>
-      <w>fa.rgraph</w>
-      <w>fa.sapa</w>
-      <w>fa.sort</w>
-      <w>fa.stats</w>
-      <w>fa2irt</w>
-      <w>fa2latex</w>
-      <w>faBy</w>
-      <w>faCor</w>
-      <w>fabricfault</w>
-      <w>fac</w>
-      <w>fac2Sparse</w>
-      <w>fac2num</w>
-      <w>fac2sparse</w>
-      <w>facet</w>
-      <w>facet_free</w>
-      <w>facet_grid</w>
-      <w>facet_null</w>
-      <w>facet_wrap</w>
-      <w>facmul</w>
-      <w>fact</w>
-      <w>factanal</w>
-      <w>facto_summarize</w>
-      <w>factoextra</w>
-      <w>factor</w>
-      <w>factor.congruence</w>
-      <w>factor.fit</w>
-      <w>factor.minres</w>
-      <w>factor.model</w>
-      <w>factor.pa</w>
-      <w>factor.plot</w>
-      <w>factor.residuals</w>
-      <w>factor.rotate</w>
-      <w>factor.scope</w>
-      <w>factor.scores</w>
-      <w>factor.stats</w>
-      <w>factor.wls</w>
-      <w>factor2character</w>
-      <w>factor2cluster</w>
-      <w>factorNames</w>
-      <w>factorValues</w>
-      <w>factorial</w>
-      <w>factorize</w>
-      <w>failure</w>
-      <w>failwith</w>
-      <w>faithful</w>
-      <w>faithfuld</w>
-      <w>family</w>
-      <w>fan.plot</w>
-      <w>fancyarrows</w>
-      <w>fanny</w>
-      <w>fansi</w>
-      <w>fansi_lines</w>
-      <w>farms</w>
-      <w>farthest.nodes</w>
-      <w>farthest_vertices</w>
-      <w>fast.1way</w>
-      <w>fastCV</w>
-      <w>fastICA</w>
-      <w>fastLm</w>
-      <w>fastLmPure</w>
-      <w>fastT</w>
-      <w>fastTps</w>
-      <w>fastTps.MLE</w>
-      <w>fastTpsMLE</w>
-      <w>fast_strptime</w>
-      <w>fasta.index</w>
-      <w>fasta.seqlengths</w>
-      <w>fastgreedy.community</w>
-      <w>fastmatch</w>
-      <w>fastme.bal</w>
-      <w>fastme.ols</w>
-      <w>fastq.geometry</w>
-      <w>fbeta</w>
-      <w>fbvalog</w>
-      <w>fbvamix</w>
-      <w>fbvaneglog</w>
-      <w>fbvbilog</w>
-      <w>fbvcalog</w>
-      <w>fbvcamix</w>
-      <w>fbvcaneglog</w>
-      <w>fbvcbilog</w>
-      <w>fbvcct</w>
-      <w>fbvchr</w>
-      <w>fbvclog</w>
-      <w>fbvcnegbilog</w>
-      <w>fbvcneglog</w>
-      <w>fbvcpot</w>
-      <w>fbvct</w>
-      <w>fbvevd</w>
-      <w>fbvhr</w>
-      <w>fbvlog</w>
-      <w>fbvnegbilog</w>
-      <w>fbvneglog</w>
-      <w>fbvpbilog</w>
-      <w>fbvpct</w>
-      <w>fbvphr</w>
-      <w>fbvplog</w>
-      <w>fbvpnegbilog</w>
-      <w>fbvpneglog</w>
-      <w>fbvpot</w>
-      <w>fbvppot</w>
-      <w>fclustIndex</w>
-      <w>fct_anon</w>
-      <w>fct_c</w>
-      <w>fct_collapse</w>
-      <w>fct_count</w>
-      <w>fct_cross</w>
-      <w>fct_drop</w>
-      <w>fct_expand</w>
-      <w>fct_explicit_na</w>
-      <w>fct_infreq</w>
-      <w>fct_inorder</w>
-      <w>fct_inseq</w>
-      <w>fct_lump</w>
-      <w>fct_lump_min</w>
-      <w>fct_match</w>
-      <w>fct_other</w>
-      <w>fct_recode</w>
-      <w>fct_relabel</w>
-      <w>fct_relevel</w>
-      <w>fct_reorder</w>
-      <w>fct_reorder2</w>
-      <w>fct_rev</w>
-      <w>fct_shift</w>
-      <w>fct_shuffle</w>
-      <w>fct_unify</w>
-      <w>fct_unique</w>
-      <w>fdHess</w>
-      <w>fdrtool</w>
-      <w>feasible</w>
-      <w>feasible.point</w>
-      <w>feather.plot</w>
-      <w>feature</w>
-      <w>featureCoverage</w>
-      <w>featureData</w>
-      <w>featureFilter</w>
-      <w>featureNames</w>
-      <w>featurePlot</w>
-      <w>features</w>
-      <w>featuretypeCounts</w>
-      <w>felCat3.ensGene.LENGTH</w>
-      <w>felCat3.geneSymbol.LENGTH</w>
-      <w>felCat3.geneid.LENGTH</w>
-      <w>felCat3.genscan.LENGTH</w>
-      <w>felCat3.nscanGene.LENGTH</w>
-      <w>felCat3.refGene.LENGTH</w>
-      <w>felCat3.sgpGene.LENGTH</w>
-      <w>felCat3.xenoRefGene.LENGTH</w>
-      <w>fetch</w>
-      <w>fetchChromSizes</w>
-      <w>fetchExtendedChromInfoFromUCSC</w>
-      <w>fetchTablesFromEnsembl</w>
-      <w>fetch_genotypes</w>
-      <w>fetch_heads</w>
-      <w>fextreme</w>
-      <w>ffCompress</w>
-      <w>fft</w>
-      <w>fgev</w>
-      <w>fgev.norm</w>
-      <w>fgev.quantile</w>
-      <w>fgl</w>
-      <w>fgsea</w>
-      <w>field</w>
-      <w>fields</w>
-      <w>fields.D</w>
-      <w>fields.color.picker</w>
-      <w>fields.convert.grid</w>
-      <w>fields.derivative.poly</w>
-      <w>fields.diagonalize</w>
-      <w>fields.diagonalize2</w>
-      <w>fields.duplicated.matrix</w>
-      <w>fields.evlpoly</w>
-      <w>fields.evlpoly2</w>
-      <w>fields.mkpoly</w>
-      <w>fields.pochdown</w>
-      <w>fields.pochup</w>
-      <w>fields.rdist.near</w>
-      <w>fields.style</w>
-      <w>fields.x.to.grid</w>
-      <w>fieldsPlotColors</w>
-      <w>fifo</w>
-      <w>fig_chunk</w>
-      <w>fig_path</w>
-      <w>file</w>
-      <w>file.access</w>
-      <w>file.append</w>
-      <w>file.choose</w>
-      <w>file.copy</w>
-      <w>file.create</w>
-      <w>file.edit</w>
-      <w>file.exists</w>
-      <w>file.info</w>
-      <w>file.info2</w>
-      <w>file.link</w>
-      <w>file.mode</w>
-      <w>file.mtime</w>
-      <w>file.path</w>
-      <w>file.remove</w>
-      <w>file.rename</w>
-      <w>file.show</w>
-      <w>file.size</w>
-      <w>file.symlink</w>
-      <w>fileAccess</w>
-      <w>fileAccess.default</w>
-      <w>fileCreate</w>
-      <w>fileInput</w>
-      <w>fileName</w>
-      <w>filePath</w>
-      <w>filePath.default</w>
-      <w>fileScan</w>
-      <w>fileSnapshot</w>
-      <w>fileUpload</w>
-      <w>file_access</w>
-      <w>file_chmod</w>
-      <w>file_chown</w>
-      <w>file_copy</w>
-      <w>file_create</w>
-      <w>file_delete</w>
-      <w>file_exists</w>
-      <w>file_ext</w>
-      <w>file_extension</w>
-      <w>file_info</w>
-      <w>file_move</w>
-      <w>file_path_as_absolute</w>
-      <w>file_path_sans_ext</w>
-      <w>file_show</w>
-      <w>file_size</w>
-      <w>file_string</w>
-      <w>file_temp</w>
-      <w>file_temp_pop</w>
-      <w>file_temp_push</w>
-      <w>file_test</w>
-      <w>file_touch</w>
-      <w>file_writer</w>
-      <w>filename</w>
-      <w>files</w>
-      <w>filesInfo</w>
-      <w>filesList</w>
-      <w>fill</w>
-      <w>fill.corner</w>
-      <w>fillCol</w>
-      <w>fillPage</w>
-      <w>fillRow</w>
-      <w>fill_</w>
-      <w>fill_palette</w>
-      <w>fillcolor</w>
-      <w>filled.contour</w>
-      <w>filledContour</w>
-      <w>fillin</w>
-      <w>filt</w>
-      <w>filter</w>
-      <w>filter.genes.without.1to1.homolog</w>
-      <w>filterBam</w>
-      <w>filterByExpr</w>
-      <w>filterByExpr.DGEList</w>
-      <w>filterByExpr.default</w>
-      <w>filterChromosomes</w>
-      <w>filterDEGs</w>
-      <w>filterFastq</w>
-      <w>filterGOByOntology</w>
-      <w>filterGeneSets</w>
-      <w>filterNull</w>
-      <w>filterOptions</w>
-      <w>filterResults</w>
-      <w>filterRules</w>
-      <w>filterSeeds</w>
-      <w>filterType</w>
-      <w>filterVarImp</w>
-      <w>filterVars</w>
-      <w>filterVcf</w>
-      <w>filterWindows</w>
-      <w>filterXY</w>
-      <w>filter_</w>
-      <w>filter_all</w>
-      <w>filter_at</w>
-      <w>filter_by_orthologs</w>
-      <w>filter_checkbox</w>
-      <w>filter_if</w>
-      <w>filter_select</w>
-      <w>filter_slider</w>
-      <w>filter_volcano</w>
-      <w>filtered_R</w>
-      <w>filtered_p</w>
-      <w>filterfun</w>
-      <w>filtering</w>
-      <w>finCenter</w>
-      <w>finalDefaultMethod</w>
-      <w>finalize</w>
-      <w>finalize.Object</w>
-      <w>finalizeSession</w>
-      <w>finalizeSession.default</w>
-      <w>finally</w>
-      <w>find</w>
-      <w>find.a0</w>
-      <w>find.cat.pos</w>
-      <w>find.dist</w>
-      <w>find.intersect</w>
-      <w>find.matches</w>
-      <w>find.package</w>
-      <w>find.skyline.epsilon</w>
-      <w>find.upcross</w>
-      <w>findAMstats</w>
-      <w>findAnnotationProbes</w>
-      <w>findChr4LL</w>
-      <w>findClass</w>
-      <w>findCompatibleOverlaps</w>
-      <w>findCorrelation</w>
-      <w>findDelta</w>
-      <w>findDependencies</w>
-      <w>findDisappeared</w>
-      <w>findDispatchMethodsS3</w>
-      <w>findDone</w>
-      <w>findErrors</w>
-      <w>findExcelGeneSymbols</w>
-      <w>findExpired</w>
-      <w>findFiles</w>
-      <w>findFiles.default</w>
-      <w>findFun</w>
-      <w>findFuncLocals</w>
-      <w>findFunction</w>
-      <w>findGhostscript</w>
-      <w>findGhostscript.System</w>
-      <w>findGlobals</w>
-      <w>findGraphicsDevice</w>
-      <w>findGraphicsDevice.System</w>
-      <w>findHTMLlinks</w>
-      <w>findHTTPHeaderEncoding</w>
-      <w>findID</w>
-      <w>findImportantPCs</w>
-      <w>findInterval</w>
-      <w>findJobs</w>
-      <w>findLargest</w>
-      <w>findLineNum</w>
-      <w>findLinearCombos</w>
-      <w>findLocals</w>
-      <w>findLocalsList</w>
-      <w>findMarkers</w>
-      <w>findMatches</w>
-      <w>findMateAlignment</w>
-      <w>findMaxima</w>
-      <w>findMethod</w>
-      <w>findMethodSignatures</w>
-      <w>findMethods</w>
-      <w>findMissingResults</w>
-      <w>findNeighbors</w>
-      <w>findNotDone</w>
-      <w>findNotErrors</w>
-      <w>findNotOnSystem</w>
-      <w>findNotRunning</w>
-      <w>findNotStarted</w>
-      <w>findNotSubmitted</w>
-      <w>findNotTerminated</w>
-      <w>findOnSystem</w>
-      <w>findOverlapPairs</w>
-      <w>findOverlaps</w>
-      <w>findPackageEnv</w>
-      <w>findPalindromes</w>
-      <w>findRange</w>
-      <w>findRecvOneTag</w>
-      <w>findRestart</w>
-      <w>findRun</w>
-      <w>findRunning</w>
-      <w>findSettings</w>
-      <w>findSettings.Settings</w>
-      <w>findSourceTraceback</w>
-      <w>findSourceTraceback.default</w>
-      <w>findSpliceOverlaps</w>
-      <w>findStarted</w>
-      <w>findSubmitted</w>
-      <w>findTerminated</w>
-      <w>findUnique</w>
-      <w>findXInclude</w>
-      <w>find_data</w>
-      <w>find_dend</w>
-      <w>find_dendrogram</w>
-      <w>find_devpackage</w>
-      <w>find_external_resources</w>
-      <w>find_gs_cmd</w>
-      <w>find_k</w>
-      <w>find_model_names</w>
-      <w>find_package_root_file</w>
-      <w>find_panel</w>
-      <w>find_remake_root_file</w>
-      <w>find_root</w>
-      <w>find_root_file</w>
-      <w>find_rshcmd</w>
-      <w>find_rstudio_root_file</w>
-      <w>find_rtools</w>
-      <w>find_testthat_root_file</w>
-      <w>findrep</w>
-      <w>finegray</w>
-      <w>fingerprint</w>
-      <w>finish</w>
-      <w>finish_glance</w>
-      <w>fintersect</w>
-      <w>fir</w>
-      <w>first</w>
-      <w>first.word</w>
-      <w>fish</w>
-      <w>fisher.test</w>
-      <w>fisherTests</w>
-      <w>fisherz</w>
-      <w>fisherz2r</w>
-      <w>fit</w>
-      <w>fit.li.wong</w>
-      <w>fit.mult.impute</w>
-      <w>fitFDist</w>
-      <w>fitFDistRobustly</w>
-      <w>fitGammaIntercept</w>
-      <w>fitNBP</w>
-      <w>fitParallel</w>
-      <w>fit_hrg</w>
-      <w>fit_power_law</w>
-      <w>fit_to_timeline</w>
-      <w>fit_xy</w>
-      <w>fitdist</w>
-      <w>fitdistcens</w>
-      <w>fitdistr</w>
-      <w>fitdistrplus</w>
-      <w>fitmixture</w>
-      <w>fitted</w>
-      <w>fitted.Krig</w>
-      <w>fitted.MArrayLM</w>
-      <w>fitted.monoreg</w>
-      <w>fitted.mselm</w>
-      <w>fitted.nlrq</w>
-      <w>fitted.rqss</w>
-      <w>fitted.selm</w>
-      <w>fitted.slm</w>
-      <w>fitted.values</w>
-      <w>fiveUTRsByTranscript</w>
-      <w>fivenum</w>
-      <w>fix</w>
-      <w>fix.bad.hgnc.symbols</w>
-      <w>fix.bad.mgi.symbols</w>
-      <w>fix.family.link</w>
-      <w>fix.family.ls</w>
-      <w>fix.family.qf</w>
-      <w>fix.family.rd</w>
-      <w>fix.family.var</w>
-      <w>fixCoordinates</w>
-      <w>fixDependence</w>
-      <w>fixInNamespace</w>
-      <w>fixMethOutliers</w>
-      <w>fixPre1.8</w>
-      <w>fix_data_frame</w>
-      <w>fix_members_attr.dendrogram</w>
-      <w>fix_mnsl</w>
-      <w>fixed</w>
-      <w>fixed.effects</w>
-      <w>fixedPage</w>
-      <w>fixedPanel</w>
-      <w>fixedRow</w>
-      <w>fixef</w>
-      <w>fixmahal</w>
-      <w>fixreg</w>
-      <w>fixsome</w>
-      <w>flag</w>
-      <w>flame</w>
-      <w>flank</w>
-      <w>flaremix.init</w>
-      <w>flaremixEM</w>
-      <w>flashClust</w>
-      <w>flatGrl</w>
-      <w>flatTable</w>
-      <w>flatten</w>
-      <w>flatten.dendrogram</w>
-      <w>flattenAssignment</w>
-      <w>flattenPanel</w>
-      <w>flatten_chr</w>
-      <w>flatten_dbl</w>
-      <w>flatten_df</w>
-      <w>flatten_dfc</w>
-      <w>flatten_dfr</w>
-      <w>flatten_int</w>
-      <w>flatten_lgl</w>
-      <w>flchain</w>
-      <w>flea</w>
-      <w>flexmix</w>
-      <w>flexmixedruns</w>
-      <w>fligner.test</w>
-      <w>flip</w>
-      <w>flip.venn</w>
-      <w>flipHorizontal</w>
-      <w>flipQuery</w>
-      <w>flipVertical</w>
-      <w>flip_leaves</w>
-      <w>flippedQuery</w>
-      <w>floating.pie</w>
-      <w>floating.pie.asp</w>
-      <w>floor</w>
-      <w>floor_date</w>
-      <w>flowLayout</w>
-      <w>flowPath</w>
-      <w>flowSorted</w>
-      <w>flower</w>
-      <w>floyd.warshall.all.pairs.sp</w>
-      <w>fluazinam</w>
-      <w>fluidPage</w>
-      <w>fluidRow</w>
-      <w>flush</w>
-      <w>flush.TextStatusBar</w>
-      <w>flush.connection</w>
-      <w>flush.console</w>
-      <w>flushDumpedAlignments</w>
-      <w>flush_console</w>
-      <w>fmatch</w>
-      <w>fmatch.hash</w>
-      <w>fmm</w>
-      <w>fn_switch</w>
-      <w>fndr.cutoff</w>
-      <w>fnsd</w>
-      <w>focal</w>
-      <w>focalWeight</w>
-      <w>fold</w>
-      <w>foldchange</w>
-      <w>foldchange2logratio</w>
-      <w>foldr</w>
-      <w>follow</w>
-      <w>font</w>
-      <w>foo</w>
-      <w>foodstamp</w>
-      <w>footsize</w>
-      <w>forName</w>
-      <w>forName.Class</w>
-      <w>forbes</w>
-      <w>forcats</w>
-      <w>force</w>
-      <w>force.integer</w>
-      <w>forceAndCall</w>
-      <w>forceGrob</w>
-      <w>forceSymmetric</w>
-      <w>force_tz</w>
-      <w>force_tzs</w>
-      <w>forder</w>
-      <w>foreach</w>
-      <w>foreign</w>
-      <w>forest.fire.game</w>
-      <w>forestplot</w>
-      <w>forgeBSgenomeDataPkg</w>
-      <w>forgeMaskedBSgenomeDataPkg</w>
-      <w>forgeMasksFiles</w>
-      <w>forgeSeqFiles</w>
-      <w>forgeSeqlengthsFile</w>
-      <w>forget</w>
-      <w>formXtViX</w>
-      <w>form_data</w>
-      <w>form_file</w>
-      <w>formalArgs</w>
-      <w>formals</w>
-      <w>format</w>
-      <w>format.AsIs</w>
-      <w>format.Date</w>
-      <w>format.POSIXct</w>
-      <w>format.POSIXlt</w>
-      <w>format.Surv</w>
-      <w>format.data.frame</w>
-      <w>format.default</w>
-      <w>format.df</w>
-      <w>format.difftime</w>
-      <w>format.factor</w>
-      <w>format.hexmode</w>
-      <w>format.info</w>
-      <w>format.libraryIQR</w>
-      <w>format.numeric_version</w>
-      <w>format.octmode</w>
-      <w>format.packageInfo</w>
-      <w>format.pval</w>
-      <w>format.summaryDefault</w>
-      <w>format.yearqtr</w>
-      <w>formatC</w>
-      <w>formatCats</w>
-      <w>formatCons</w>
-      <w>formatCurrency</w>
-      <w>formatDL</w>
-      <w>formatDate</w>
-      <w>formatDateTime</w>
-      <w>formatDescription</w>
-      <w>formatOL</w>
-      <w>formatPercentage</w>
-      <w>formatR</w>
-      <w>formatRound</w>
-      <w>formatSep</w>
-      <w>formatSignif</w>
-      <w>formatSpMatrix</w>
-      <w>formatSparseM</w>
-      <w>formatStackTrace</w>
-      <w>formatString</w>
-      <w>formatStyle</w>
-      <w>formatTestStats</w>
-      <w>formatUL</w>
-      <w>format_csv</w>
-      <w>format_csv2</w>
-      <w>format_delim</w>
-      <w>format_format</w>
-      <w>format_from_ext</w>
-      <w>format_from_signature</w>
-      <w>format_funusage</w>
-      <w>format_sumstats_for_magma</w>
-      <w>format_tagged_na</w>
-      <w>format_tsv</w>
-      <w>format_type_sum</w>
-      <w>formatdescribeSingle</w>
-      <w>formula</w>
-      <w>formula.gam</w>
-      <w>formula.nlrq</w>
-      <w>formula.rq</w>
-      <w>fortify</w>
-      <w>fortify.zoo</w>
-      <w>fortify_map</w>
-      <w>forward</w>
-      <w>forwardsolve</w>
-      <w>forwardsolve.spam</w>
-      <w>fot</w>
-      <w>fourCellsFromXY</w>
-      <w>fourfoldplot</w>
-      <w>foverlaps</w>
-      <w>fox</w>
-      <w>fparse</w>
-      <w>fpc</w>
-      <w>fpclusters</w>
-      <w>fpclusters.mfpc</w>
-      <w>fpclusters.rfpc</w>
-      <w>fpiter</w>
-      <w>fpkm</w>
-      <w>fplot</w>
-      <w>fpm</w>
-      <w>fpmi</w>
-      <w>fpot</w>
-      <w>fpot.norm</w>
-      <w>fpot.quantile</w>
-      <w>fr1.ensGene.LENGTH</w>
-      <w>fr1.genscan.LENGTH</w>
-      <w>fr2.ensGene.LENGTH</w>
-      <w>fractions</w>
-      <w>fragment</w>
-      <w>frailty</w>
-      <w>frailty.gamma</w>
-      <w>frailty.gaussian</w>
-      <w>frailty.t</w>
-      <w>frame</w>
-      <w>frameApply</w>
-      <w>frameGrob</w>
-      <w>frame_data</w>
-      <w>frame_matrix</w>
-      <w>franceMapEnv</w>
-      <w>frank</w>
-      <w>frankv</w>
-      <w>fread</w>
-      <w>freduce</w>
-      <w>free</w>
-      <w>freeny</w>
-      <w>freezePane</w>
-      <w>freezeReactiveVal</w>
-      <w>freezeReactiveValue</w>
-      <w>french_fries</w>
-      <w>freq</w>
-      <w>freq.array</w>
-      <w>frequency</w>
-      <w>frequency.polygon</w>
-      <w>frets</w>
-      <w>friedman.test</w>
-      <w>frjd</w>
-      <w>frollmean</w>
-      <w>from</w>
-      <w>fromCellDataSet</w>
-      <w>fromDisk</w>
-      <w>fromExpression</w>
-      <w>fromGXL</w>
-      <w>fromJSON</w>
-      <w>fromList</w>
-      <w>fromTo</w>
-      <w>from_adjacency</w>
-      <w>from_data_frame</w>
-      <w>from_edgelist</w>
-      <w>from_incidence_matrix</w>
-      <w>from_literal</w>
-      <w>from_rmarkdown</w>
-      <w>from_wd</w>
-      <w>frontier</w>
-      <w>fruchtermanReingoldForceDirectedLayout</w>
-      <w>fruit</w>
-      <w>fry</w>
-      <w>fry.DGEList</w>
-      <w>fry.default</w>
-      <w>fs</w>
-      <w>fs.boundary</w>
-      <w>fs.test</w>
-      <w>fs_bytes</w>
-      <w>fs_path</w>
-      <w>fs_perms</w>
-      <w>fsetdiff</w>
-      <w>fsetequal</w>
-      <w>fsort</w>
-      <w>fstats</w>
-      <w>fsva</w>
-      <w>ftM2adjM</w>
-      <w>ftM2graphNEL</w>
-      <w>ftM2int</w>
-      <w>ftable</w>
-      <w>ftemp</w>
-      <w>ftpUpload</w>
-      <w>ftupwr</w>
-      <w>ftuss</w>
-      <w>fudge2</w>
-      <w>fuks</w>
-      <w>full.score</w>
-      <w>fullRank</w>
-      <w>full_bipartite_graph</w>
-      <w>full_citation_graph</w>
-      <w>full_graph</w>
-      <w>full_join</w>
-      <w>full_seq</w>
-      <w>fullaxis</w>
-      <w>fullgrid</w>
-      <w>fullseq</w>
-      <w>fully_trained</w>
-      <w>funEnv</w>
-      <w>functionBody</w>
-      <w>functionGrob</w>
-      <w>function_new</w>
-      <w>functional</w>
-      <w>functions</w>
-      <w>funion</w>
-      <w>funs</w>
-      <w>funs_</w>
-      <w>furc</w>
-      <w>futile.options</w>
-      <w>future</w>
-      <w>future.apply</w>
-      <w>futureAssign</w>
-      <w>futureCall</w>
-      <w>futureOf</w>
-      <w>future_Map</w>
-      <w>future_apply</w>
-      <w>future_by</w>
-      <w>future_eapply</w>
-      <w>future_lapply</w>
-      <w>future_mapply</w>
-      <w>future_replicate</w>
-      <w>future_sapply</w>
-      <w>future_tapply</w>
-      <w>future_vapply</w>
-      <w>futures</w>
-      <w>fuzzy.ebam</w>
-      <w>fuzzy.stat</w>
-      <w>fvarLabels</w>
-      <w>fvarMetadata</w>
-      <w>fviz</w>
-      <w>fviz_add</w>
-      <w>fviz_ca</w>
-      <w>fviz_ca_biplot</w>
-      <w>fviz_ca_col</w>
-      <w>fviz_ca_row</w>
-      <w>fviz_cluster</w>
-      <w>fviz_contrib</w>
-      <w>fviz_cos2</w>
-      <w>fviz_dend</w>
-      <w>fviz_dist</w>
-      <w>fviz_eig</w>
-      <w>fviz_ellipses</w>
-      <w>fviz_famd</w>
-      <w>fviz_famd_ind</w>
-      <w>fviz_famd_var</w>
-      <w>fviz_gap_stat</w>
-      <w>fviz_hmfa</w>
-      <w>fviz_hmfa_group</w>
-      <w>fviz_hmfa_ind</w>
-      <w>fviz_hmfa_ind_starplot</w>
-      <w>fviz_hmfa_quali_biplot</w>
-      <w>fviz_hmfa_quali_var</w>
-      <w>fviz_hmfa_quanti_var</w>
-      <w>fviz_hmfa_var</w>
-      <w>fviz_mca</w>
-      <w>fviz_mca_biplot</w>
-      <w>fviz_mca_ind</w>
-      <w>fviz_mca_var</w>
-      <w>fviz_mclust</w>
-      <w>fviz_mclust_bic</w>
-      <w>fviz_mfa</w>
-      <w>fviz_mfa_axes</w>
-      <w>fviz_mfa_group</w>
-      <w>fviz_mfa_ind</w>
-      <w>fviz_mfa_ind_starplot</w>
-      <w>fviz_mfa_quali_biplot</w>
-      <w>fviz_mfa_quali_var</w>
-      <w>fviz_mfa_quanti_var</w>
-      <w>fviz_mfa_var</w>
-      <w>fviz_nbclust</w>
-      <w>fviz_pca</w>
-      <w>fviz_pca_biplot</w>
-      <w>fviz_pca_contrib</w>
-      <w>fviz_pca_ind</w>
-      <w>fviz_pca_var</w>
-      <w>fviz_screeplot</w>
-      <w>fviz_silhouette</w>
-      <w>fwer2fdr</w>
-      <w>fwer2gfwer</w>
-      <w>fwer2tppfp</w>
-      <w>fwf_cols</w>
-      <w>fwf_empty</w>
-      <w>fwf_positions</w>
-      <w>fwf_widths</w>
-      <w>fwrite</w>
-      <w>fyff</w>
-      <w>g2r</w>
-      <w>gEdit</w>
-      <w>gEditList</w>
-      <w>gList</w>
-      <w>gPath</w>
-      <w>gTree</w>
-      <w>gafs</w>
-      <w>gafs.default</w>
-      <w>gafsControl</w>
-      <w>gafs_initial</w>
-      <w>gafs_lrSelection</w>
-      <w>gafs_raMutation</w>
-      <w>gafs_rwSelection</w>
-      <w>gafs_spCrossover</w>
-      <w>gafs_tourSelection</w>
-      <w>gafs_uCrossover</w>
-      <w>gain</w>
-      <w>galGal2.ensGene.LENGTH</w>
-      <w>galGal2.geneSymbol.LENGTH</w>
-      <w>galGal2.geneid.LENGTH</w>
-      <w>galGal2.genscan.LENGTH</w>
-      <w>galGal2.refGene.LENGTH</w>
-      <w>galGal2.sgpGene.LENGTH</w>
-      <w>galGal3.ensGene.LENGTH</w>
-      <w>galGal3.geneSymbol.LENGTH</w>
-      <w>galGal3.genscan.LENGTH</w>
-      <w>galGal3.nscanGene.LENGTH</w>
-      <w>galGal3.refGene.LENGTH</w>
-      <w>galGal3.xenoRefGene.LENGTH</w>
-      <w>galaxies</w>
-      <w>galton</w>
-      <w>gam</w>
-      <w>gam.check</w>
-      <w>gam.control</w>
-      <w>gam.fit</w>
-      <w>gam.fit3</w>
-      <w>gam.fit5.post.proc</w>
-      <w>gam.lf</w>
-      <w>gam.outer</w>
-      <w>gam.reparam</w>
-      <w>gam.side</w>
-      <w>gam.slist</w>
-      <w>gam.vcomp</w>
-      <w>gam2derivative</w>
-      <w>gam2objective</w>
-      <w>gamFormula</w>
-      <w>gamFuncs</w>
-      <w>gamLine</w>
-      <w>gamScores</w>
-      <w>gamSim</w>
-      <w>gamlss.etamu</w>
-      <w>gamlss.gH</w>
-      <w>gamm</w>
-      <w>gamma</w>
-      <w>gamma.dispersion</w>
-      <w>gamma.shape</w>
-      <w>gammaFitEM</w>
-      <w>gammaStat</w>
-      <w>gammamix.init</w>
-      <w>gammamixEM</w>
-      <w>gantt.chart</w>
-      <w>gap.barplot</w>
-      <w>gap.boxplot</w>
-      <w>gap.plot</w>
-      <w>gapFilter</w>
-      <w>gaphunter</w>
-      <w>gapply</w>
-      <w>gaps</w>
-      <w>gasAcu1.ensGene.LENGTH</w>
-      <w>gasAcu1.nscanGene.LENGTH</w>
-      <w>gasoline</w>
-      <w>gasprice</w>
-      <w>gastric</w>
-      <w>gather</w>
-      <w>gather_</w>
-      <w>gather_attrs</w>
-      <w>gaucov</w>
-      <w>gaulss</w>
-      <w>gauss.cov</w>
-      <w>gauss.quad</w>
-      <w>gauss.quad.prob</w>
-      <w>gaussEstMultiple</w>
-      <w>gaussian</w>
-      <w>gaussian.lvm</w>
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-      <w>gene</w>
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-      <w>geneCounts</w>
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-      <w>geneCovariate</w>
-      <w>geneData</w>
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-      <w>geneIds</w>
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-      <w>geneList</w>
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-      <w>geneModels</w>
-      <w>geneNames</w>
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-      <w>geneSelectionFun</w>
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-      <w>geneSim</w>
-      <w>geneSymbols</w>
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-      <w>geneexp</w>
-      <w>genefilter</w>
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-      <w>generate_controlled_bootstrap_geneset</w>
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-      <w>genericBeadIntensityPlot</w>
-      <w>genericSAXHandlers</w>
-      <w>generics</w>
-      <w>genes</w>
-      <w>genesInTerm</w>
-      <w>genescale</w>
-      <w>genesymbol</w>
-      <w>genki</w>
-      <w>genkme</w>
-      <w>genkus</w>
-      <w>genme</w>
-      <w>geno</w>
-      <w>genome</w>
-      <w>genomeBrowsers</w>
-      <w>genomeBuilds</w>
-      <w>genomeName</w>
-      <w>genomeStyles</w>
-      <w>genotype</w>
-      <w>genotypeCodesToNucleotides</w>
-      <w>genotypeToSnpMatrix</w>
-      <w>genotypes</w>
-      <w>genus</w>
-      <w>geo2neighbor</w>
-      <w>geom</w>
-      <w>geom2trace</w>
-      <w>geom_abline</w>
-      <w>geom_area</w>
-      <w>geom_bar</w>
-      <w>geom_beeswarm</w>
-      <w>geom_bin2d</w>
-      <w>geom_blank</w>
-      <w>geom_boxplot</w>
-      <w>geom_col</w>
-      <w>geom_contour</w>
-      <w>geom_count</w>
-      <w>geom_crossbar</w>
-      <w>geom_curve</w>
-      <w>geom_density</w>
-      <w>geom_density2d</w>
-      <w>geom_density_2d</w>
-      <w>geom_density_line</w>
-      <w>geom_density_ridges</w>
-      <w>geom_density_ridges2</w>
-      <w>geom_density_ridges_gradient</w>
-      <w>geom_dotplot</w>
-      <w>geom_errorbar</w>
-      <w>geom_errorbarh</w>
-      <w>geom_exec</w>
-      <w>geom_freqpoly</w>
-      <w>geom_hex</w>
-      <w>geom_histogram</w>
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-      <w>geom_line</w>
-      <w>geom_linerange</w>
-      <w>geom_map</w>
-      <w>geom_path</w>
-      <w>geom_point</w>
-      <w>geom_pointrange</w>
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-      <w>geom_rect</w>
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-      <w>geom_rug</w>
-      <w>geom_segment</w>
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-      <w>geom_sf_label</w>
-      <w>geom_sf_text</w>
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-      <w>geom_step</w>
-      <w>geom_text</w>
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-      <w>geom_tile</w>
-      <w>geom_violin</w>
-      <w>geom_vline</w>
-      <w>geom_vridgeline</w>
-      <w>geometric.mean</w>
-      <w>geometry</w>
-      <w>geomorphology</w>
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-      <w>germany.plot</w>
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-      <w>get.Tn</w>
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-      <w>get.adjedgelist</w>
-      <w>get.adjlist</w>
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-      <w>get.celfile.dates</w>
-      <w>get.celltype.table</w>
-      <w>get.data.frame</w>
-      <w>get.diameter</w>
-      <w>get.edge</w>
-      <w>get.edge.attribute</w>
-      <w>get.edge.ids</w>
-      <w>get.edgelist</w>
-      <w>get.edges</w>
-      <w>get.gantt.info</w>
-      <w>get.gpar</w>
-      <w>get.graph.attribute</w>
-      <w>get.incidence</w>
-      <w>get.index</w>
-      <w>get.knn</w>
-      <w>get.knnx</w>
-      <w>get.length.of.longest.string</w>
-      <w>get.rectangle</w>
-      <w>get.segs</w>
-      <w>get.shortest.paths</w>
-      <w>get.soil.texture</w>
-      <w>get.stochastic</w>
-      <w>get.symbol.from.homologID</w>
-      <w>get.tablepos</w>
-      <w>get.triprop</w>
-      <w>get.var</w>
-      <w>get.venn.partitions</w>
-      <w>get.vertex.attribute</w>
-      <w>get0</w>
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-      <w>get2rowHeads</w>
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-      <w>getAnnMap</w>
-      <w>getAnnotation</w>
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-      <w>getAssayDataNameSubstitutions</w>
-      <w>getAssignedVar</w>
-      <w>getAttributeNames</w>
-      <w>getAuthor</w>
-      <w>getAuthor.Package</w>
-      <w>getBM</w>
-      <w>getBMFeatureAnnos</w>
-      <w>getBMlist</w>
-      <w>getBSgenome</w>
-      <w>getBSseq</w>
-      <w>getBackgroundFrequencies</w>
-      <w>getBarString</w>
-      <w>getBarString.ProgressBar</w>
-      <w>getBarcodes</w>
-      <w>getBaseFont</w>
-      <w>getBatchesByOverlapsFromOnDiskLongTable</w>
-      <w>getBatchesBySeqnameFromOnDiskLongTable</w>
-      <w>getBatchesFromOnDiskLongTable</w>
-      <w>getBatchesFromOnDiskLongTable_old</w>
-      <w>getBeadData</w>
-      <w>getBestChunkDims</w>
-      <w>getBestIndex</w>
-      <w>getBestOverlaps</w>
-      <w>getBestTest</w>
-      <w>getBeta</w>
-      <w>getBibstyle</w>
-      <w>getBimapFilters</w>
-      <w>getBinaryURL</w>
-      <w>getBioColor</w>
-      <w>getBioRegion</w>
-      <w>getBiocMirror</w>
-      <w>getBiocRepos</w>
-      <w>getBitIndicators</w>
-      <w>getBlocks</w>
-      <w>getBoundary</w>
-      <w>getBroadSets</w>
-      <w>getBuiltinDate</w>
-      <w>getBuiltinDate.GString</w>
-      <w>getBuiltinDatetime</w>
-      <w>getBuiltinDatetime.GString</w>
-      <w>getBuiltinHostname</w>
-      <w>getBuiltinHostname.GString</w>
-      <w>getBuiltinOs</w>
-      <w>getBuiltinOs.GString</w>
-      <w>getBuiltinPid</w>
-      <w>getBuiltinPid.GString</w>
-      <w>getBuiltinRhome</w>
-      <w>getBuiltinRhome.GString</w>
-      <w>getBuiltinRversion</w>
-      <w>getBuiltinRversion.GString</w>
-      <w>getBuiltinTime</w>
-      <w>getBuiltinTime.GString</w>
-      <w>getBuiltinUsername</w>
-      <w>getBuiltinUsername.GString</w>
-      <w>getBundle</w>
-      <w>getBundle.Package</w>
-      <w>getBundlePackages</w>
-      <w>getBundlePackages.Package</w>
-      <w>getCN</w>
-      <w>getCRANmirrors</w>
-      <w>getCTSS</w>
-      <w>getCVSTTest</w>
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-      <w>getCallingDLLe</w>
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-      <w>getCharacters.Arguments</w>
-      <w>getChildrenStrings</w>
-      <w>getChipInfo</w>
-      <w>getChrInfo</w>
-      <w>getChromInfoFromBiomart</w>
-      <w>getChromInfoFromUCSC</w>
-      <w>getChromosomesByOrganism</w>
-      <w>getClass</w>
-      <w>getClass1</w>
-      <w>getClassDef</w>
-      <w>getClassName</w>
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-      <w>getClassS4Usage.Rdoc</w>
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-      <w>getCol</w>
-      <w>getCommonPrefix</w>
-      <w>getCompilerOption</w>
-      <w>getComplete</w>
-      <w>getConfig</w>
-      <w>getConnection</w>
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-      <w>getDate.Package</w>
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-      <w>getDependency</w>
-      <w>getDescription</w>
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-      <w>getEvent</w>
-      <w>getEvidence</w>
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-      <w>getGEOInfo</w>
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-      <w>getGEOgenomeVersion</w>
-      <w>getGEOspecies</w>
-      <w>getGI</w>
-      <w>getGO</w>
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-      <w>getGene</w>
-      <w>getGeneKEGGLinks</w>
-      <w>getGeneRegionTrackForGviz</w>
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-      <w>getGenomeAndMask</w>
-      <w>getGenomeFaFile</w>
-      <w>getGenomicRatioSetFromGEO</w>
-      <w>getGlobalsAndPackages</w>
-      <w>getGmt</w>
-      <w>getGraphRoot</w>
-      <w>getGraphicsEvent</w>
-      <w>getGraphicsEventEnv</w>
-      <w>getGreen</w>
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-      <w>getGridTopology</w>
-      <w>getGrob</w>
-      <w>getGroup</w>
-      <w>getGroupMembers</w>
-      <w>getGroups</w>
-      <w>getGroupsFormula</w>
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-      <w>getHDF5DumpCompressionLevel</w>
-      <w>getHDF5DumpDir</w>
-      <w>getHDF5DumpFile</w>
-      <w>getHDF5DumpName</w>
-      <w>getHMedian</w>
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-      <w>getHdf5Version</w>
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-      <w>getJobIds</w>
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-      <w>getJobParamDf</w>
-      <w>getJobResources</w>
-      <w>getJobs</w>
-      <w>getK</w>
-      <w>getKEGGFrameData</w>
-      <w>getKEGGPathwayNames</w>
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-      <w>getKeywords</w>
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-      <w>getLL</w>
-      <w>getLRT</w>
-      <w>getLRT.lm</w>
-      <w>getLRT.mer</w>
-      <w>getLRT.merMod</w>
-      <w>getLabel</w>
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-      <w>getPolygonsPolygonsSlot</w>
-      <w>getPolygonsplotOrderSlot</w>
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-      <w>getPriorN</w>
-      <w>getProbeDataAffy</w>
-      <w>getProbeData_1lq</w>
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-      <w>getRaw.GString</w>
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-      <w>getRccUrl.RccViolationException</w>
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-      <w>getRow</w>
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-      <w>getRowsByIndexFromOnDiskLongTable_old</w>
-      <w>getRowsFromOnDiskLongTable</w>
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-      <w>ggdotplot</w>
-      <w>ggdraw</w>
-      <w>ggduo</w>
-      <w>ggecdf</w>
-      <w>ggerrorplot</w>
-      <w>ggexport</w>
-      <w>ggfacet</w>
-      <w>ggfortify</w>
-      <w>ggfreqScatter</w>
-      <w>ggfreqplot</w>
-      <w>gghistogram</w>
-      <w>ggindplot</w>
-      <w>gglegend</w>
-      <w>ggline</w>
-      <w>ggmaplot</w>
-      <w>ggmatrix</w>
-      <w>ggmatrix_gtable</w>
-      <w>ggmatrix_progress</w>
-      <w>ggnet</w>
-      <w>ggnet2</w>
-      <w>ggnetworkmap</w>
-      <w>ggnostic</w>
-      <w>ggpaired</w>
-      <w>ggpairs</w>
-      <w>ggpar</w>
-      <w>ggparagraph</w>
-      <w>ggparcoord</w>
-      <w>ggpie</w>
-      <w>ggplot</w>
-      <w>ggplot.gafs</w>
-      <w>ggplot.safs</w>
-      <w>ggplot2</w>
-      <w>ggplot2like</w>
-      <w>ggplot2like.opts</w>
-      <w>ggplotGrob</w>
-      <w>ggplot_add</w>
-      <w>ggplot_build</w>
-      <w>ggplot_gtable</w>
-      <w>ggplotly</w>
-      <w>ggproto</w>
-      <w>ggproto_parent</w>
-      <w>ggpubr</w>
-      <w>ggqqplot</w>
-      <w>ggrepel</w>
-      <w>ggridges</w>
-      <w>ggsave</w>
-      <w>ggscatmat</w>
-      <w>ggscatter</w>
-      <w>ggscatterhist</w>
-      <w>ggsci</w>
-      <w>ggscreeplot</w>
-      <w>ggsignif</w>
-      <w>ggstripchart</w>
-      <w>ggsurv</w>
-      <w>ggtext</w>
-      <w>ggtexttable</w>
-      <w>ggtitle</w>
-      <w>ggts</w>
-      <w>ggtsdiag</w>
-      <w>ggviolin</w>
-      <w>gh</w>
-      <w>gh_first</w>
-      <w>gh_last</w>
-      <w>gh_next</w>
-      <w>gh_prev</w>
-      <w>gh_tree_remote</w>
-      <w>gh_whoami</w>
-      <w>gilgais</w>
-      <w>gini</w>
-      <w>ginla</w>
-      <w>ginv</w>
-      <w>girth</w>
-      <w>git2r</w>
-      <w>git_config_files</w>
-      <w>git_credentials</w>
-      <w>git_protocol</w>
-      <w>git_remotes</w>
-      <w>git_sitrep</w>
-      <w>git_vaccinate</w>
-      <w>github_document</w>
-      <w>github_pat</w>
-      <w>github_pull</w>
-      <w>github_release</w>
-      <w>github_token</w>
-      <w>gitlab_pat</w>
-      <w>gkgamma</w>
-      <w>gl</w>
-      <w>glFrequency</w>
-      <w>glance</w>
-      <w>glass</w>
-      <w>glayer</w>
-      <w>glayer_</w>
-      <w>glb</w>
-      <w>glb.algebraic</w>
-      <w>glb.fa</w>
-      <w>glc</w>
-      <w>glcInitializeSplitEigen</w>
-      <w>glcInitializeSplitFanny</w>
-      <w>glcInitializeSplitHClust</w>
-      <w>glcSplit</w>
-      <w>glcSplitCriterionBIC</w>
-      <w>glcSplitCriterionBICICL</w>
-      <w>glcSplitCriterionJustRecordEverything</w>
-      <w>glcSplitCriterionLRT</w>
-      <w>glcSplitCriterionLevelWtdBIC</w>
-      <w>glcSubTree</w>
-      <w>glcTree</w>
-      <w>glcTreeApply</w>
-      <w>glcTreeLeafClasses</w>
-      <w>glcTreeLeafMatrix</w>
-      <w>glcTreeOverallBIC</w>
-      <w>glimpse</w>
-      <w>glinearModel</w>
-      <w>glm</w>
-      <w>glm.control</w>
-      <w>glm.convert</w>
-      <w>glm.diag</w>
-      <w>glm.diag.plots</w>
-      <w>glm.fit</w>
-      <w>glm.nb</w>
-      <w>glm.scoretest</w>
-      <w>glm4</w>
-      <w>glmFit</w>
-      <w>glmFit.DGEList</w>
-      <w>glmFit.default</w>
-      <w>glmLC</w>
-      <w>glmLRT</w>
-      <w>glmQLFTest</w>
-      <w>glmQLFit</w>
-      <w>glmQLFit.DGEList</w>
-      <w>glmQLFit.default</w>
-      <w>glmTreat</w>
-      <w>glmgam.fit</w>
-      <w>glmmPQL</w>
-      <w>glmnb.fit</w>
-      <w>glmrob</w>
-      <w>glmrobBY.control</w>
-      <w>glmrobMT.control</w>
-      <w>glmrobMqle.control</w>
-      <w>glob2rx</w>
-      <w>globalVariables</w>
-      <w>globalenv</w>
-      <w>globals</w>
-      <w>globalsByName</w>
-      <w>globalsOf</w>
-      <w>gls</w>
-      <w>gls.series</w>
-      <w>glsApVar</w>
-      <w>glsControl</w>
-      <w>glsEstimate</w>
-      <w>glsStruct</w>
-      <w>glue</w>
-      <w>glue_col</w>
-      <w>glue_collapse</w>
-      <w>glue_data</w>
-      <w>glue_data_col</w>
-      <w>glue_data_sql</w>
-      <w>glue_sql</w>
-      <w>glyphplot</w>
-      <w>glyphs</w>
-      <w>gmdc</w>
-      <w>gmmhd</w>
-      <w>gmmhdClassify</w>
-      <w>gmmhdClusterCores</w>
-      <w>gmtPathways</w>
-      <w>gnls</w>
-      <w>gnlsControl</w>
-      <w>gnlsStruct</w>
-      <w>gnm</w>
-      <w>gnp</w>
-      <w>gnuplot</w>
-      <w>goBarplot</w>
-      <w>goDag</w>
-      <w>goSim</w>
-      <w>goSlim</w>
-      <w>goana</w>
-      <w>goana.DGEExact</w>
-      <w>goana.DGELRT</w>
-      <w>goana.MArrayLM</w>
-      <w>goana.default</w>
-      <w>godata</w>
-      <w>gof</w>
-      <w>gofstat</w>
-      <w>golden.section.search</w>
-      <w>golub</w>
-      <w>gometh</w>
-      <w>goodSNP</w>
-      <w>goodTuring</w>
-      <w>goodTuringPlot</w>
-      <w>goodTuringProportions</w>
-      <w>google_search</w>
-      <w>gopher.D</w>
-      <w>gorder</w>
-      <w>goseq</w>
-      <w>got</w>
-      <w>gotbl</w>
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-      <w>gower_topn</w>
-      <w>gpar</w>
-      <w>gpclibPermit</w>
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-      <w>gplot.hexbin</w>
-      <w>gplots</w>
-      <w>gprofile</w>
-      <w>gqtest</w>
-      <w>grDevices</w>
-      <w>grImport</w>
-      <w>grSoftVersion</w>
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-      <w>grab_legend</w>
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-      <w>grangertest</w>
-      <w>grangertest.default</w>
-      <w>granges</w>
-      <w>grangesPairsForDotplot</w>
-      <w>graph</w>
-      <w>graph.adhesion</w>
-      <w>graph.adjacency</w>
-      <w>graph.adjlist</w>
-      <w>graph.atlas</w>
-      <w>graph.attributes</w>
-      <w>graph.automorphisms</w>
-      <w>graph.bfs</w>
-      <w>graph.bipartite</w>
-      <w>graph.cohesion</w>
-      <w>graph.complementer</w>
-      <w>graph.compose</w>
-      <w>graph.coreness</w>
-      <w>graph.count.isomorphisms.vf2</w>
-      <w>graph.count.subisomorphisms.vf2</w>
-      <w>graph.data.frame</w>
-      <w>graph.de.bruijn</w>
-      <w>graph.density</w>
-      <w>graph.dfs</w>
-      <w>graph.difference</w>
-      <w>graph.disjoint.union</w>
-      <w>graph.diversity</w>
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-      <w>graph.incidence</w>
-      <w>graph.intersection</w>
-      <w>graph.isoclass</w>
-      <w>graph.isoclass.subgraph</w>
-      <w>graph.isocreate</w>
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-      <w>graph.kautz</w>
-      <w>graph.knn</w>
-      <w>graph.laplacian</w>
-      <w>graph.lattice</w>
-      <w>graph.lcf</w>
-      <w>graph.maxflow</w>
-      <w>graph.mincut</w>
-      <w>graph.motifs</w>
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-      <w>graph.tree</w>
-      <w>graph.union</w>
-      <w>graph.var</w>
-      <w>graph2SparseM</w>
-      <w>graph2T</w>
-      <w>graph2lvm</w>
-      <w>graphAM</w>
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-      <w>graphData</w>
-      <w>graphDataDefaults</w>
-      <w>graphExamples</w>
-      <w>graphGenerator</w>
-      <w>graphIntersect</w>
-      <w>graphLayout</w>
-      <w>graphNEL</w>
-      <w>graphRenderInfo</w>
-      <w>graphUnion</w>
-      <w>graph_</w>
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-      <w>graph_attr_names</w>
-      <w>graph_from_adj_list</w>
-      <w>graph_from_adjacency_matrix</w>
-      <w>graph_from_atlas</w>
-      <w>graph_from_data_frame</w>
-      <w>graph_from_edgelist</w>
-      <w>graph_from_graphdb</w>
-      <w>graph_from_graphnel</w>
-      <w>graph_from_incidence_matrix</w>
-      <w>graph_from_isomorphism_class</w>
-      <w>graph_from_lcf</w>
-      <w>graph_from_literal</w>
-      <w>graph_id</w>
-      <w>graph_version</w>
-      <w>graphics</w>
-      <w>graphics.off</w>
-      <w>graphlet_basis</w>
-      <w>graphlet_proj</w>
-      <w>graphlets</w>
-      <w>graphlets.candidate.basis</w>
-      <w>graphlets.project</w>
-      <w>graphs_from_cohesive_blocks</w>
-      <w>graphvizCapabilities</w>
-      <w>graphvizVersion</w>
-      <w>grav</w>
-      <w>gravity</w>
-      <w>gray</w>
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-      <w>grconvertY</w>
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-      <w>greenChannel</w>
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-      <w>grenander</w>
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-      <w>grepl</w>
-      <w>grey</w>
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-      <w>grey_pal</w>
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-      <w>grglist</w>
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-      <w>grid.xaxis</w>
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-      <w>gridBase</w>
-      <w>gridDistance</w>
-      <w>gridExtra</w>
-      <w>gridFIG</w>
-      <w>gridIndex2nb</w>
-      <w>gridOMI</w>
-      <w>gridPAR</w>
-      <w>gridPLT</w>
-      <w>grid_trace2</w>
-      <w>grid_zoom</w>
-      <w>gridat</w>
-      <w>gridc</w>
-      <w>gridded</w>
-      <w>gridlines</w>
-      <w>gridparameters</w>
-      <w>gridr</w>
-      <w>grids</w>
-      <w>grob</w>
-      <w>grobAscent</w>
-      <w>grobDescent</w>
-      <w>grobHeight</w>
-      <w>grobName</w>
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-      <w>grobTree</w>
-      <w>grobWidth</w>
-      <w>grobX</w>
-      <w>grobY</w>
-      <w>grobify</w>
-      <w>groessen_MvsF</w>
-      <w>groundbeef</w>
-      <w>group</w>
-      <w>group2NA</w>
-      <w>groupGOTerms</w>
-      <w>groupKFold</w>
-      <w>groupReport</w>
-      <w>group_by</w>
-      <w>group_by_</w>
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-      <w>group_by_at</w>
-      <w>group_by_if</w>
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-      <w>group_ids</w>
-      <w>group_indices</w>
-      <w>group_indices_</w>
-      <w>group_size</w>
-      <w>group_vars</w>
-      <w>groupedData</w>
-      <w>groupedHeatmap</w>
-      <w>grouped_df</w>
-      <w>grouping</w>
-      <w>groupingsets</w>
-      <w>grouplengths</w>
-      <w>groupn</w>
-      <w>grouprank</w>
-      <w>groups</w>
-      <w>groups_by_filter</w>
-      <w>groups_factor</w>
-      <w>growing</w>
-      <w>growing.random.game</w>
-      <w>growth</w>
-      <w>growthofmoney</w>
-      <w>gsameth</w>
-      <w>gseDGN</w>
-      <w>gseDO</w>
-      <w>gseNCG</w>
-      <w>gseaplot</w>
-      <w>gseattperm</w>
-      <w>gsfilter</w>
-      <w>gsize</w>
-      <w>gsminfo</w>
-      <w>gss_cat</w>
-      <w>gstring</w>
-      <w>gstring.GString</w>
-      <w>gstring.default</w>
-      <w>gsub</w>
-      <w>gsub_dir</w>
-      <w>gsub_ext</w>
-      <w>gsub_file</w>
-      <w>gsub_files</w>
-      <w>gsummary</w>
-      <w>gsva</w>
-      <w>gt</w>
-      <w>gtable</w>
-      <w>gtable_add_col_space</w>
-      <w>gtable_add_cols</w>
-      <w>gtable_add_grob</w>
-      <w>gtable_add_padding</w>
-      <w>gtable_add_row_space</w>
-      <w>gtable_add_rows</w>
-      <w>gtable_cbind</w>
-      <w>gtable_col</w>
-      <w>gtable_col_spacer</w>
-      <w>gtable_combine</w>
-      <w>gtable_filter</w>
-      <w>gtable_height</w>
-      <w>gtable_matrix</w>
-      <w>gtable_rbind</w>
-      <w>gtable_remove_grobs</w>
-      <w>gtable_row</w>
-      <w>gtable_row_spacer</w>
-      <w>gtable_show_layout</w>
-      <w>gtable_squash_cols</w>
-      <w>gtable_squash_rows</w>
-      <w>gtable_trim</w>
-      <w>gtable_width</w>
-      <w>gtools</w>
-      <w>guessMIMEType</w>
-      <w>guess_encoding</w>
-      <w>guess_fo</w>
-      <w>guess_formats</w>
-      <w>guess_media</w>
-      <w>guess_parser</w>
-      <w>guess_type</w>
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-      <w>guide_colourbar</w>
-      <w>guide_gengrob</w>
-      <w>guide_geom</w>
-      <w>guide_legend</w>
-      <w>guide_merge</w>
-      <w>guide_train</w>
-      <w>guides</w>
-      <w>gunzip</w>
-      <w>gunzip.default</w>
-      <w>gursoyAtunLayout</w>
-      <w>guttman</w>
-      <w>gvhd10</w>
-      <w>gxlTreeNEL</w>
-      <w>gzAzimuth</w>
-      <w>gzcon</w>
-      <w>gzfile</w>
-      <w>gzip</w>
-      <w>gzip.default</w>
-      <w>h.alpha.n</w>
-      <w>h1</w>
-      <w>h2</w>
-      <w>h3</w>
-      <w>h4</w>
-      <w>h5</w>
-      <w>h5const</w>
-      <w>h5constType</w>
-      <w>h5createAttribute</w>
-      <w>h5createDataset</w>
-      <w>h5createFile</w>
-      <w>h5createGroup</w>
-      <w>h5default</w>
-      <w>h5dump</w>
-      <w>h5errorHandling</w>
-      <w>h5listIdentifier</w>
-      <w>h5ls</w>
-      <w>h5read</w>
-      <w>h5readAttributes</w>
-      <w>h5save</w>
-      <w>h5set_extent</w>
-      <w>h5validObjects</w>
-      <w>h5version</w>
-      <w>h5write</w>
-      <w>h5write.default</w>
-      <w>h5writeAttribute</w>
-      <w>h5writeAttribute.array</w>
-      <w>h5writeAttribute.character</w>
-      <w>h5writeAttribute.double</w>
-      <w>h5writeAttribute.integer</w>
-      <w>h5writeAttribute.logical</w>
-      <w>h5writeAttribute.matrix</w>
-      <w>h5writeDataset</w>
-      <w>h5writeDataset.array</w>
-      <w>h5writeDataset.character</w>
-      <w>h5writeDataset.data.frame</w>
-      <w>h5writeDataset.double</w>
-      <w>h5writeDataset.integer</w>
-      <w>h5writeDataset.list</w>
-      <w>h5writeDataset.logical</w>
-      <w>h5writeDataset.matrix</w>
-      <w>h6</w>
-      <w>haberman</w>
-      <w>half.image</w>
-      <w>half.range.mode</w>
-      <w>halfspacen</w>
-      <w>hamming.distance</w>
-      <w>hamming.window</w>
-      <w>hampelPsi</w>
-      <w>handle</w>
-      <w>handle_cookies</w>
-      <w>handle_data</w>
-      <w>handle_find</w>
-      <w>handle_reset</w>
-      <w>handle_setform</w>
-      <w>handle_setheaders</w>
-      <w>handle_setopt</w>
-      <w>hang.dendrogram</w>
-      <w>hanning.window</w>
-      <w>happy</w>
-      <w>hard.rejection</w>
-      <w>hardFilters</w>
-      <w>harmonic.mean</w>
-      <w>harvtest</w>
-      <w>has</w>
-      <w>has.multiple</w>
-      <w>has.singles</w>
-      <w>hasAllFlinks</w>
-      <w>hasArg</w>
-      <w>hasArg2</w>
-      <w>hasAssay</w>
-      <w>hasAttributes</w>
-      <w>hasBeenSmoothed</w>
-      <w>hasColorConsole</w>
-      <w>hasEnvar</w>
-      <w>hasField</w>
-      <w>hasField.BasicObject</w>
-      <w>hasField.Object</w>
-      <w>hasFun</w>
-      <w>hasGOannote</w>
-      <w>hasLetterAt</w>
-      <w>hasLoadAction</w>
-      <w>hasMethod</w>
-      <w>hasMethods</w>
-      <w>hasMultiProbes</w>
-      <w>hasName</w>
-      <w>hasNames</w>
-      <w>hasOnlyBaseLetters</w>
-      <w>hasOption</w>
-      <w>hasOption.Options</w>
-      <w>hasPackageRegistry</w>
-      <w>hasProteinData</w>
-      <w>hasRNG</w>
-      <w>hasSingleProbes</w>
-      <w>hasTerms</w>
-      <w>hasTsp</w>
-      <w>hasUrlProtocol</w>
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-      <w>hasValues</w>
-      <w>hasVarArgs</w>
-      <w>has_args</w>
-      <w>has_attr</w>
-      <w>has_build_tools</w>
-      <w>has_cache</w>
-      <w>has_color</w>
-      <w>has_compiler</w>
-      <w>has_component_in_attribute</w>
-      <w>has_content</w>
-      <w>has_ctl</w>
-      <w>has_devel</w>
-      <w>has_dir</w>
-      <w>has_dirname</w>
-      <w>has_edgePar</w>
-      <w>has_element</w>
-      <w>has_extension</w>
-      <w>has_file</w>
-      <w>has_file_pattern</w>
-      <w>has_internet</w>
-      <w>has_latex</w>
-      <w>has_name</w>
-      <w>has_nodePar</w>
-      <w>has_role</w>
-      <w>has_rownames</w>
-      <w>has_rtools</w>
-      <w>has_sgr</w>
-      <w>has_style</w>
-      <w>has_tests</w>
-      <w>has_type</w>
-      <w>hash</w>
-      <w>hashCode</w>
-      <w>hashCode.BasicObject</w>
-      <w>hashCode.Object</w>
-      <w>hashCode.default</w>
-      <w>hashfile</w>
-      <w>haskey</w>
-      <w>hat</w>
-      <w>hatMat</w>
-      <w>hatmatrix</w>
-      <w>hatvalues</w>
-      <w>haven</w>
-      <w>hazuh</w>
-      <w>hbk</w>
-      <w>hboxplot</w>
-      <w>hbvalog</w>
-      <w>hbvamix</w>
-      <w>hbvaneglog</w>
-      <w>hbvbilog</w>
-      <w>hbvct</w>
-      <w>hbvevd</w>
-      <w>hbvhr</w>
-      <w>hbvlog</w>
-      <w>hbvnegbilog</w>
-      <w>hbvneglog</w>
-      <w>hc</w>
-      <w>hc.score</w>
-      <w>hc.thresh</w>
-      <w>hcE</w>
-      <w>hcEEE</w>
-      <w>hcEII</w>
-      <w>hcV</w>
-      <w>hcVII</w>
-      <w>hcVVV</w>
-      <w>hccm</w>
-      <w>hcell2xy</w>
-      <w>hcell2xyInt</w>
-      <w>hcl</w>
-      <w>hcl_color_picker</w>
-      <w>hcl_palettes</w>
-      <w>hcl_wizard</w>
-      <w>hclass</w>
-      <w>hclcolorpicker</w>
-      <w>hclplot</w>
-      <w>hclust</w>
-      <w>hclust.bclust</w>
-      <w>hclustCBI</w>
-      <w>hclusttreeCBI</w>
-      <w>hclwizard</w>
-      <w>hcube</w>
-      <w>hcut</w>
-      <w>hdiffplot</w>
-      <w>hdquantile</w>
-      <w>hdr</w>
-      <w>hdrlevels</w>
-      <w>head</w>
-      <w>head.DataTable</w>
-      <w>head.LLint</w>
-      <w>head.Vector</w>
-      <w>head.matrix</w>
-      <w>head.spam</w>
-      <w>headTail</w>
-      <w>head_of</w>
-      <w>head_print</w>
-      <w>head_while</w>
-      <w>header</w>
-      <w>header.NullVerbose</w>
-      <w>header.Verbose</w>
-      <w>headerPanel</w>
-      <w>headerTabix</w>
-      <w>headers</w>
-      <w>headtail</w>
-      <w>health</w>
-      <w>heart</w>
-      <w>heat.colors</w>
-      <w>heat.ob</w>
-      <w>heatDiagram</w>
-      <w>heat_hcl</w>
-      <w>heatdiagram</w>
-      <w>heatmap</w>
-      <w>heatmap.2</w>
-      <w>heavisine</w>
-      <w>heavytail</w>
-      <w>heckbert</w>
-      <w>hedenfalk</w>
-      <w>heidel.diag</w>
-      <w>heightDetails</w>
-      <w>heights</w>
-      <w>heights_per_k.dendrogram</w>
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-      <w>help.ebam</w>
-      <w>help.finda0</w>
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-      <w>help.sam</w>
-      <w>help.search</w>
-      <w>help.start</w>
-      <w>helpMethods</w>
-      <w>helpText</w>
-      <w>hemophilia</w>
-      <w>hendricks</w>
-      <w>here</w>
-      <w>hessian</w>
-      <w>het.diagram</w>
-      <w>heuristicC</w>
-      <w>hex</w>
-      <w>hex2RGB</w>
-      <w>hexGraphPaper</w>
-      <w>hexList</w>
-      <w>hexMA.loess</w>
-      <w>hexTapply</w>
-      <w>hexVP.abline</w>
-      <w>hexVP.loess</w>
-      <w>hexViewport</w>
-      <w>hexagon</w>
-      <w>hexbin</w>
-      <w>hexbinplot</w>
-      <w>hexcoords</w>
-      <w>hexlegendGrob</w>
-      <w>hexplom</w>
-      <w>hexpolygon</w>
-      <w>hfti</w>
-      <w>hg16.acembly.LENGTH</w>
-      <w>hg16.ensGene.LENGTH</w>
-      <w>hg16.exoniphy.LENGTH</w>
-      <w>hg16.geneSymbol.LENGTH</w>
-      <w>hg16.geneid.LENGTH</w>
-      <w>hg16.genscan.LENGTH</w>
-      <w>hg16.knownGene.LENGTH</w>
-      <w>hg16.refGene.LENGTH</w>
-      <w>hg16.sgpGene.LENGTH</w>
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-      <w>hg17.acescan.LENGTH</w>
-      <w>hg17.ccdsGene.LENGTH</w>
-      <w>hg17.ensGene.LENGTH</w>
-      <w>hg17.exoniphy.LENGTH</w>
-      <w>hg17.geneSymbol.LENGTH</w>
-      <w>hg17.geneid.LENGTH</w>
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-      <w>hg17.knownGene.LENGTH</w>
-      <w>hg17.refGene.LENGTH</w>
-      <w>hg17.sgpGene.LENGTH</w>
-      <w>hg17.vegaGene.LENGTH</w>
-      <w>hg17.vegaPseudoGene.LENGTH</w>
-      <w>hg17.xenoRefGene.LENGTH</w>
-      <w>hg18.acembly.LENGTH</w>
-      <w>hg18.acescan.LENGTH</w>
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-      <w>hg18.ensGene.LENGTH</w>
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-      <w>hg18.knownGene.LENGTH</w>
-      <w>hg18.knownGeneOld3.LENGTH</w>
-      <w>hg18.refGene.LENGTH</w>
-      <w>hg18.sgpGene.LENGTH</w>
-      <w>hg18.sibGene.LENGTH</w>
-      <w>hg18.xenoRefGene.LENGTH</w>
-      <w>hg18ToHg19</w>
-      <w>hg19.ccdsGene.LENGTH</w>
-      <w>hg19.ensGene.LENGTH</w>
-      <w>hg19.exoniphy.LENGTH</w>
-      <w>hg19.geneSymbol.LENGTH</w>
-      <w>hg19.islands</w>
-      <w>hg19.knownGene.LENGTH</w>
-      <w>hg19.nscanGene.LENGTH</w>
-      <w>hg19.refGene.LENGTH</w>
-      <w>hg19.xenoRefGene.LENGTH</w>
-      <w>hg19Ideogram</w>
-      <w>hg19IdeogramCyto</w>
-      <w>hgByChroms</w>
-      <w>hgCLengths</w>
-      <w>hgnc.table</w>
-      <w>hgridcent</w>
-      <w>hgu95AProbLocs</w>
-      <w>hgu95Achroloc</w>
-      <w>hgu95Achrom</w>
-      <w>hgu95All</w>
-      <w>hgu95Asym</w>
-      <w>hi_andre</w>
-      <w>hi_html</w>
-      <w>hi_latex</w>
-      <w>hidden</w>
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-      <w>hideTab</w>
-      <w>hide_colorbar</w>
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-      <w>hide_legend</w>
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-      <w>hist2d</w>
-      <w>histBxp</w>
-      <w>histBy</w>
-      <w>histSpike</w>
-      <w>histSpikeg</w>
-      <w>histStack</w>
-      <w>histbackback</w>
-      <w>histboxp</w>
-      <w>histboxpM</w>
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-      <w>hivtree.newick</w>
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-      <w>hkmeans</w>
-      <w>hkmeans_tree</w>
-      <w>hlog</w>
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-      <w>hm27.SNP.colors</w>
-      <w>hm27.controls</w>
-      <w>hm27.ordering</w>
-      <w>hm27ToHg19</w>
-      <w>hm450.controls</w>
-      <w>hm450.ordering</w>
-      <w>hm450k.rsProbes</w>
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-      <w>hms_trans</w>
-      <w>hobbies</w>
-      <w>hobbs</w>
-      <w>hoeffd</w>
-      <w>holdoutRF</w>
-      <w>holiday</w>
-      <w>holidayLONDON</w>
-      <w>holidayNERC</w>
-      <w>holidayNYSE</w>
-      <w>holidayTSX</w>
-      <w>holidayZURICH</w>
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-      <w>homoHGID</w>
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-      <w>hook_movecode</w>
-      <w>hook_optipng</w>
-      <w>hook_pdfcrop</w>
-      <w>hook_plot_asciidoc</w>
-      <w>hook_plot_custom</w>
-      <w>hook_plot_html</w>
-      <w>hook_plot_md</w>
-      <w>hook_plot_rst</w>
-      <w>hook_plot_tex</w>
-      <w>hook_plot_textile</w>
-      <w>hook_pngquant</w>
-      <w>hook_purl</w>
-      <w>hook_r2swf</w>
-      <w>hook_scianimator</w>
-      <w>hook_toggle</w>
-      <w>hook_try</w>
-      <w>horizonplot</w>
-      <w>host_extract</w>
-      <w>hour</w>
-      <w>hours</w>
-      <w>housetasks</w>
-      <w>housing</w>
-      <w>hoverOpts</w>
-      <w>how</w>
-      <w>howmanytrees</w>
-      <w>hpaste</w>
-      <w>hpaste.default</w>
-      <w>hprabclust</w>
-      <w>hprdAsigH</w>
-      <w>hpsd_genes</w>
-      <w>hr</w>
-      <w>hrg</w>
-      <w>hrg.consensus</w>
-      <w>hrg.create</w>
-      <w>hrg.dendrogram</w>
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-      <w>hrg.game</w>
-      <w>hrg.predict</w>
-      <w>hrg_tree</w>
-      <w>hsearch_db</w>
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-      <w>hsearch_db_keywords</w>
-      <w>hsize</w>
-      <w>hsize.numeric</w>
-      <w>hsize.object_size</w>
-      <w>hsmooth</w>
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-      <w>hsv_palette</w>
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-      <w>htmlDependencies</w>
-      <w>htmlDependency</w>
-      <w>htmlEscape</w>
-      <w>htmlGreek</w>
-      <w>htmlOutput</w>
-      <w>htmlPage</w>
-      <w>htmlParse</w>
-      <w>htmlPreserve</w>
-      <w>htmlReport</w>
-      <w>htmlSN</w>
-      <w>htmlSpecial</w>
-      <w>htmlSpecialType</w>
-      <w>htmlTable</w>
-      <w>htmlTableWidget</w>
-      <w>htmlTableWidgetOutput</w>
-      <w>htmlTemplate</w>
-      <w>htmlTranslate</w>
-      <w>htmlTreeParse</w>
-      <w>htmlVerbatim</w>
-      <w>html_code_block</w>
-      <w>html_dependency_bootstrap</w>
-      <w>html_dependency_font_awesome</w>
-      <w>html_dependency_highlightjs</w>
-      <w>html_dependency_ionicons</w>
-      <w>html_dependency_jquery</w>
-      <w>html_dependency_jqueryui</w>
-      <w>html_dependency_pagedtable</w>
-      <w>html_dependency_tocify</w>
-      <w>html_document</w>
-      <w>html_document_base</w>
-      <w>html_esc</w>
-      <w>html_fragment</w>
-      <w>html_notebook</w>
-      <w>html_notebook_metadata</w>
-      <w>html_notebook_output_code</w>
-      <w>html_notebook_output_html</w>
-      <w>html_notebook_output_img</w>
-      <w>html_notebook_output_png</w>
-      <w>html_pretty</w>
-      <w>html_print</w>
-      <w>html_structure</w>
-      <w>html_vignette</w>
-      <w>htmlpage</w>
-      <w>htmltools</w>
-      <w>htmlwidgets</w>
-      <w>httpDELETE</w>
-      <w>httpGET</w>
-      <w>httpHEAD</w>
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-      <w>httpPOST</w>
-      <w>httpPUT</w>
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-      <w>http_date</w>
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-      <w>http_search</w>
-      <w>http_status</w>
-      <w>http_type</w>
-      <w>httpcode</w>
-      <w>httpuv</w>
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-      <w>httr_options</w>
-      <w>hub.score</w>
-      <w>hubCache</w>
-      <w>hubDate</w>
-      <w>hubUrl</w>
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-      <w>hubble</w>
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-      <w>huber</w>
-      <w>huberM</w>
-      <w>huberPsi</w>
-      <w>hubers</w>
-      <w>hudson</w>
-      <w>hue_pal</w>
-      <w>hue_slice</w>
-      <w>humanReadable</w>
-      <w>hvc2mnsl</w>
-      <w>hwrite</w>
-      <w>hwriteImage</w>
-      <w>hwriter</w>
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-      <w>hyperGTest</w>
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-      <w>iDMR</w>
-      <w>iapply</w>
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-      <w>ica.R.par</w>
-      <w>icafast</w>
-      <w>icaimax</w>
-      <w>icajade</w>
-      <w>icaplot</w>
-      <w>icasamp</w>
-      <w>icendata</w>
-      <w>ichar</w>
-      <w>icl</w>
-      <w>iclust</w>
-      <w>iclust.diagram</w>
-      <w>iclust.sort</w>
-      <w>icon</w>
-      <w>iconv</w>
-      <w>iconvlist</w>
-      <w>icount</w>
-      <w>icountn</w>
-      <w>icr</w>
-      <w>icuGetCollate</w>
-      <w>icuSetCollate</w>
-      <w>id</w>
-      <w>id2name</w>
-      <w>id2seq</w>
-      <w>idConverter</w>
-      <w>idFilter</w>
-      <w>idTrack</w>
-      <w>idType</w>
-      <w>id_genes</w>
-      <w>idata.frame</w>
-      <w>idconv</w>
-      <w>ident</w>
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-      <w>identicalCRS</w>
-      <w>identical_graphs</w>
-      <w>identifier</w>
-      <w>identify</w>
-      <w>identify.map</w>
-      <w>identifyControlBeads</w>
-      <w>identity</w>
-      <w>identity_pal</w>
-      <w>identity_trans</w>
-      <w>identity_transformer</w>
-      <w>ideo</w>
-      <w>ideoCyto</w>
-      <w>ideogramPlot</w>
-      <w>idf</w>
-      <w>idiv</w>
-      <w>idplot</w>
-      <w>ids</w>
-      <w>ids2indices</w>
-      <w>idx2dimnames</w>
-      <w>idxstatsBam</w>
-      <w>ie_get_proxy_for_url</w>
-      <w>ie_proxy_info</w>
-      <w>if_else</w>
-      <w>ifelse</w>
-      <w>ifelse.zoo</w>
-      <w>ifelse2</w>
-      <w>ignore.strand</w>
-      <w>igpoly</w>
-      <w>igraph</w>
-      <w>igraph.arpack.default</w>
-      <w>igraph.console</w>
-      <w>igraph.drl.coarsen</w>
-      <w>igraph.drl.coarsest</w>
-      <w>igraph.drl.default</w>
-      <w>igraph.drl.final</w>
-      <w>igraph.drl.refine</w>
-      <w>igraph.eigen.default</w>
-      <w>igraph.from.graphNEL</w>
-      <w>igraph.lvm</w>
-      <w>igraph.options</w>
-      <w>igraph.sample</w>
-      <w>igraph.shape.noclip</w>
-      <w>igraph.shape.noplot</w>
-      <w>igraph.to.graphNEL</w>
-      <w>igraph.version</w>
-      <w>igraph_demo</w>
-      <w>igraph_opt</w>
-      <w>igraph_options</w>
-      <w>igraph_test</w>
-      <w>igraph_version</w>
-      <w>igraphdemo</w>
-      <w>igraphtest</w>
-      <w>igsva</w>
-      <w>ihw</w>
-      <w>iid</w>
-      <w>illumina450Gr</w>
-      <w>illuminaBackground</w>
-      <w>illuminaEPICGr</w>
-      <w>illuminaForeground</w>
-      <w>illuminaHumanv4</w>
-      <w>illuminaHumanv4.db</w>
-      <w>illuminaHumanv4ACCNUM</w>
-      <w>illuminaHumanv4ALIAS2PROBE</w>
-      <w>illuminaHumanv4ARRAYADDRESS</w>
-      <w>illuminaHumanv4CHR</w>
-      <w>illuminaHumanv4CHRLENGTHS</w>
-      <w>illuminaHumanv4CHRLOC</w>
-      <w>illuminaHumanv4CHRLOCEND</w>
-      <w>illuminaHumanv4CODINGZONE</w>
-      <w>illuminaHumanv4ENSEMBL</w>
-      <w>illuminaHumanv4ENSEMBL2PROBE</w>
-      <w>illuminaHumanv4ENSEMBLREANNOTATED</w>
-      <w>illuminaHumanv4ENTREZID</w>
-      <w>illuminaHumanv4ENTREZREANNOTATED</w>
-      <w>illuminaHumanv4ENZYME</w>
-      <w>illuminaHumanv4ENZYME2PROBE</w>
-      <w>illuminaHumanv4GENENAME</w>
-      <w>illuminaHumanv4GENOMICLOCATION</w>
-      <w>illuminaHumanv4GO</w>
-      <w>illuminaHumanv4GO2ALLPROBES</w>
-      <w>illuminaHumanv4GO2PROBE</w>
-      <w>illuminaHumanv4MAP</w>
-      <w>illuminaHumanv4MAPCOUNTS</w>
-      <w>illuminaHumanv4NUID</w>
-      <w>illuminaHumanv4OMIM</w>
-      <w>illuminaHumanv4ORGANISM</w>
-      <w>illuminaHumanv4ORGPKG</w>
-      <w>illuminaHumanv4OTHERGENOMICMATCHES</w>
-      <w>illuminaHumanv4OVERLAPPINGSNP</w>
-      <w>illuminaHumanv4PATH</w>
-      <w>illuminaHumanv4PATH2PROBE</w>
-      <w>illuminaHumanv4PFAM</w>
-      <w>illuminaHumanv4PMID</w>
-      <w>illuminaHumanv4PMID2PROBE</w>
-      <w>illuminaHumanv4PROBEQUALITY</w>
-      <w>illuminaHumanv4PROBESEQUENCE</w>
-      <w>illuminaHumanv4PROSITE</w>
-      <w>illuminaHumanv4REFSEQ</w>
-      <w>illuminaHumanv4REPEATMASK</w>
-      <w>illuminaHumanv4REPORTERGROUPID</w>
-      <w>illuminaHumanv4REPORTERGROUPNAME</w>
-      <w>illuminaHumanv4SECONDMATCHES</w>
-      <w>illuminaHumanv4SYMBOL</w>
-      <w>illuminaHumanv4SYMBOLREANNOTATED</w>
-      <w>illuminaHumanv4UNIGENE</w>
-      <w>illuminaHumanv4UNIPROT</w>
-      <w>illuminaHumanv4_dbInfo</w>
-      <w>illuminaHumanv4_dbconn</w>
-      <w>illuminaHumanv4_dbfile</w>
-      <w>illuminaHumanv4_dbschema</w>
-      <w>illuminaHumanv4fullReannotation</w>
-      <w>illuminaHumanv4listNewMappings</w>
-      <w>illuminaOutlierMethod</w>
-      <w>illuminaSharpen</w>
-      <w>illuminaio</w>
-      <w>ilogit2</w>
-      <w>image</w>
-      <w>image.AAbin</w>
-      <w>image.DNAbin</w>
-      <w>image.default</w>
-      <w>image.plot</w>
-      <w>image.smooth</w>
-      <w>image.spam</w>
-      <w>image2Grid</w>
-      <w>imageAnalysisPath</w>
-      <w>imageMap</w>
-      <w>imageOutput</w>
-      <w>imagePlotInfo</w>
-      <w>imageScale</w>
-      <w>image_uri</w>
-      <w>imageplot</w>
-      <w>imageplot.info</w>
-      <w>imageplot.setup</w>
-      <w>imageplot3by2</w>
-      <w>images</w>
-      <w>imap</w>
-      <w>imap_chr</w>
-      <w>imap_dbl</w>
-      <w>imap_dfc</w>
-      <w>imap_dfr</w>
-      <w>imap_int</w>
-      <w>imap_lgl</w>
-      <w>img</w>
-      <w>imgur_upload</w>
-      <w>immer</w>
-      <w>imp.moments</w>
-      <w>imp.prob</w>
-      <w>imp.quantile</w>
-      <w>imp.weights</w>
-      <w>imp_vars</w>
-      <w>implicitGeneric</w>
-      <w>import</w>
-      <w>import.2bit</w>
-      <w>import.bed</w>
-      <w>import.bed15</w>
-      <w>import.bedGraph</w>
-      <w>import.bw</w>
-      <w>import.chain</w>
-      <w>import.gff</w>
-      <w>import.gff1</w>
-      <w>import.gff2</w>
-      <w>import.gff3</w>
-      <w>import.ucsc</w>
-      <w>import.wig</w>
-      <w>importBam</w>
-      <w>importConvertDateTime</w>
-      <w>importData</w>
-      <w>importIntoEnv</w>
-      <w>importMethyIDAT</w>
-      <w>importPandaMatlab</w>
-      <w>importPublicData</w>
-      <w>importScore</w>
-      <w>import_list</w>
-      <w>importance</w>
-      <w>importance_pvalues</w>
-      <w>imports_env</w>
-      <w>improveProb</w>
-      <w>improvedCV2</w>
-      <w>impute</w>
-      <w>impute.knn</w>
-      <w>impute.transcan</w>
-      <w>imputeData</w>
-      <w>imputePairs</w>
-      <w>in.land.grid</w>
-      <w>in.out</w>
-      <w>in.poly</w>
-      <w>in.poly.grid</w>
-      <w>inAnyInterval</w>
-      <w>inAnyInterval.numeric</w>
-      <w>inEdges</w>
-      <w>inMemory</w>
-      <w>inSide</w>
-      <w>inSweave</w>
-      <w>in_circle</w>
-      <w>in_dir</w>
-      <w>in_gamut</w>
-      <w>in_repository</w>
-      <w>inbagg</w>
-      <w>incProgress</w>
-      <w>inc_to_inc</w>
-      <w>inchol</w>
-      <w>incidence</w>
-      <w>incident</w>
-      <w>incident_edges</w>
-      <w>inclass</w>
-      <w>includeCSS</w>
-      <w>includeHTML</w>
-      <w>includeMarkdown</w>
-      <w>includeScript</w>
-      <w>includeText</w>
-      <w>include_app</w>
-      <w>include_graphics</w>
-      <w>include_url</w>
-      <w>includes</w>
-      <w>includes_to_pandoc_args</w>
-      <w>incmatrix</w>
-      <w>income</w>
-      <w>increase</w>
-      <w>increase.ProgressBar</w>
-      <w>incremental.components</w>
-      <w>indel</w>
-      <w>indentSpaces</w>
-      <w>indent_print</w>
-      <w>independence.number</w>
-      <w>independent.vertex.sets</w>
-      <w>index</w>
-      <w>index.dynrq</w>
-      <w>index2char</w>
-      <w>index2vec</w>
-      <w>indexBam</w>
-      <w>indexBcf</w>
-      <w>indexByRow</w>
-      <w>indexFa</w>
-      <w>indexProbes</w>
-      <w>indexTabix</w>
-      <w>indexVcf</w>
-      <w>index_remove_bypath</w>
-      <w>indian_liver_patient_1vs2</w>
-      <w>indian_liver_patient_FvsM</w>
-      <w>indices</w>
-      <w>indices2xy</w>
-      <w>indoorenv</w>
-      <w>induced.subgraph</w>
-      <w>inducedGraph</w>
-      <w>inducedTermGraph</w>
-      <w>induced_subgraph</w>
-      <w>indx</w>
-      <w>infIndexPlot</w>
-      <w>inferno</w>
-      <w>infert</w>
-      <w>infile1</w>
-      <w>infile2</w>
-      <w>infimalRank</w>
-      <w>influence</w>
-      <w>influence.gam</w>
-      <w>influence.measures</w>
-      <w>influenceIndexPlot</w>
-      <w>influencePlot</w>
-      <w>info</w>
-      <w>infoBox</w>
-      <w>infoBoxOutput</w>
-      <w>infoCheck</w>
-      <w>infomap.community</w>
-      <w>information</w>
-      <w>infotheo</w>
-      <w>inheritedSlotNames</w>
-      <w>inherits</w>
-      <w>inherits.Assert</w>
-      <w>inherits.default</w>
-      <w>inheritsFrom</w>
-      <w>inheritsFrom.Assert</w>
-      <w>inhulln</w>
-      <w>ini</w>
-      <w>init</w>
-      <w>init.incremental.components</w>
-      <w>initDefaultClusterOptions</w>
-      <w>initExtension</w>
-      <w>initFieldArgs</w>
-      <w>initFlexmix</w>
-      <w>initRNGstreamNode</w>
-      <w>initRefFields</w>
-      <w>init_cpp</w>
-      <w>init_oauth1.0</w>
-      <w>init_oauth2.0</w>
-      <w>initfun</w>
-      <w>initial.sp</w>
-      <w>initialize</w>
-      <w>initializeProject</w>
-      <w>initseq</w>
-      <w>injectHardMask</w>
-      <w>injectSNPs</w>
-      <w>inject_funs</w>
-      <w>inlearn</w>
-      <w>inline</w>
-      <w>inlineCSS</w>
-      <w>inline_expr</w>
-      <w>inmChoice</w>
-      <w>inner_join</w>
-      <w>inout.hex</w>
-      <w>inpIDMapper</w>
-      <w>inpoly</w>
-      <w>inputFiles</w>
-      <w>inputFilesType</w>
-      <w>inputPanel</w>
-      <w>inputcheck1</w>
-      <w>inrange</w>
-      <w>insect</w>
-      <w>insensitive</w>
-      <w>insert</w>
-      <w>insert.NA</w>
-      <w>insert.default</w>
-      <w>insertBeadData</w>
-      <w>insertClassMethods</w>
-      <w>insertImage</w>
-      <w>insertMethod</w>
-      <w>insertPlot</w>
-      <w>insertSectionData</w>
-      <w>insertSource</w>
-      <w>insertTab</w>
-      <w>insertText</w>
-      <w>insertUI</w>
-      <w>insert_all_ref</w>
-      <w>insert_citeOnly</w>
-      <w>insert_ref</w>
-      <w>insert_xaxis_grob</w>
-      <w>insert_yaxis_grob</w>
-      <w>insertion</w>
-      <w>inset</w>
-      <w>inset2</w>
-      <w>inspect</w>
-      <w>inspect_Rd</w>
-      <w>inspect_Rdbib</w>
-      <w>inspect_Rdclass</w>
-      <w>inspect_Rdfun</w>
-      <w>inspect_Rdmethods</w>
-      <w>inspect_args</w>
-      <w>inspect_clmethods</w>
-      <w>inspect_signatures</w>
-      <w>inspect_slots</w>
-      <w>inspect_usage</w>
-      <w>inst</w>
-      <w>install</w>
-      <w>install.extrapackages</w>
-      <w>install.extras</w>
-      <w>install.packages</w>
-      <w>installExprFunction</w>
-      <w>installFoundDepends</w>
-      <w>installPackages</w>
-      <w>installPackages.default</w>
-      <w>installPackagesOnSSHWorkers</w>
-      <w>installSuggests</w>
-      <w>installXLSXsupport</w>
-      <w>install_bioc</w>
-      <w>install_bitbucket</w>
-      <w>install_cran</w>
-      <w>install_deps</w>
-      <w>install_dev</w>
-      <w>install_dev_deps</w>
-      <w>install_dir</w>
-      <w>install_formats</w>
-      <w>install_git</w>
-      <w>install_github</w>
-      <w>install_gitlab</w>
-      <w>install_local</w>
-      <w>install_svn</w>
-      <w>install_tinytex</w>
-      <w>install_url</w>
-      <w>install_version</w>
-      <w>installed.SNPs</w>
-      <w>installed.genomes</w>
-      <w>installed.packages</w>
-      <w>int2col</w>
-      <w>int2ftM</w>
-      <w>intToBin</w>
-      <w>intToBits</w>
-      <w>intToChar</w>
-      <w>intToChar.default</w>
-      <w>intToHex</w>
-      <w>intToOct</w>
-      <w>intToUtf8</w>
-      <w>int_aligns</w>
-      <w>int_diff</w>
-      <w>int_end</w>
-      <w>int_flip</w>
-      <w>int_length</w>
-      <w>int_overlaps</w>
-      <w>int_shift</w>
-      <w>int_standardize</w>
-      <w>int_start</w>
-      <w>integer</w>
-      <w>integer_dc</w>
-      <w>integral</w>
-      <w>integrate</w>
-      <w>integrate.xy</w>
-      <w>integrations</w>
-      <w>intensities.IB</w>
-      <w>intensities.M</w>
-      <w>intensities.OOB</w>
-      <w>intensities.OOB.allelic</w>
-      <w>intensities.U</w>
-      <w>intensitiesByChannel</w>
-      <w>intensity</w>
-      <w>interGeneCorrelation</w>
-      <w>interaction</w>
-      <w>interaction.plot</w>
-      <w>interactive</w>
-      <w>interactiveDisplayBase</w>
-      <w>interactiveTable</w>
-      <w>interbattery</w>
-      <w>intercept</w>
-      <w>interconnected.islands.game</w>
-      <w>intergenic</w>
-      <w>interinformation</w>
-      <w>interleave</w>
-      <w>interp</w>
-      <w>interp.boxplot</w>
-      <w>interp.median</w>
-      <w>interp.q</w>
-      <w>interp.qplot.by</w>
-      <w>interp.quantiles</w>
-      <w>interp.quart</w>
-      <w>interp.quartiles</w>
-      <w>interp.surface</w>
-      <w>interp.surface.grid</w>
-      <w>interp.values</w>
-      <w>interpSpline</w>
-      <w>interpolate</w>
-      <w>interpolate_cvd_transform</w>
-      <w>interpret.gam</w>
-      <w>interrupt</w>
-      <w>intersect</w>
-      <w>intersect.Vector</w>
-      <w>intersectColumns</w>
-      <w>intersectDiagram</w>
-      <w>intersectRows</w>
-      <w>intersect_trees</w>
-      <w>intersection</w>
-      <w>intersection2</w>
-      <w>intersectlist</w>
-      <w>intersectmatrix</w>
-      <w>intersectn</w>
-      <w>intersects</w>
-      <w>interval</w>
-      <w>interval_complement</w>
-      <w>interval_difference</w>
-      <w>interval_included</w>
-      <w>interval_intersection</w>
-      <w>interval_overlap</w>
-      <w>interval_union</w>
-      <w>intervals</w>
-      <w>intervalsToSeq</w>
-      <w>intervalsToSeq.matrix</w>
-      <w>intfix</w>
-      <w>intisasc</w>
-      <w>intisdesc</w>
-      <w>intraIDMapper</w>
-      <w>intraspotCorrelation</w>
-      <w>intrle</w>
-      <w>intronicParts</w>
-      <w>intronsByTranscript</w>
-      <w>inv.logit</w>
-      <w>inv.seq</w>
-      <w>invPerm</w>
-      <w>invResPlot</w>
-      <w>invTranEstimate</w>
-      <w>invTranPlot</w>
-      <w>invalid</w>
-      <w>invalidateLater</w>
-      <w>invchisq</w>
-      <w>inverse</w>
-      <w>inverse.gaussian</w>
-      <w>inverse.rle</w>
-      <w>inverseFunction</w>
-      <w>inverseList</w>
-      <w>inverseResponsePlot</w>
-      <w>inverseVST</w>
-      <w>invertStrand</w>
-      <w>invertTabulated</w>
-      <w>invert_match</w>
-      <w>invisible</w>
-      <w>invoke</w>
-      <w>invokeRestart</w>
-      <w>invokeRestartInteractively</w>
-      <w>invoke_map</w>
-      <w>invoke_map_chr</w>
-      <w>invoke_map_dbl</w>
-      <w>invoke_map_df</w>
-      <w>invoke_map_dfc</w>
-      <w>invoke_map_dfr</w>
-      <w>invoke_map_int</w>
-      <w>invoke_map_lgl</w>
-      <w>invt</w>
-      <w>invvar</w>
-      <w>ions</w>
-      <w>ioslides_presentation</w>
-      <w>ip</w>
-      <w>ipFamily</w>
-      <w>ipcid</w>
-      <w>ipclock</w>
-      <w>ipclocked</w>
-      <w>ipcremove</w>
-      <w>ipcreset</w>
-      <w>ipctrylock</w>
-      <w>ipcunlock</w>
-      <w>ipcvalue</w>
-      <w>ipcyield</w>
-      <w>ipop</w>
-      <w>ipred</w>
-      <w>ipredStats</w>
-      <w>ipredbagg</w>
-      <w>ipredknn</w>
-      <w>iqitems</w>
-      <w>iqr</w>
-      <w>iqrDiff</w>
-      <w>iqrFun</w>
-      <w>irbinom</w>
-      <w>iread.table</w>
-      <w>ireadLines</w>
-      <w>irequire</w>
-      <w>iris</w>
-      <w>iris3</w>
-      <w>iris_setosavsversicolor</w>
-      <w>iris_setosavsvirginica</w>
-      <w>iris_versicolorvsvirginica</w>
-      <w>irish_ed_MvsF</w>
-      <w>irlba</w>
-      <w>irnbinom</w>
-      <w>irnorm</w>
-      <w>irpois</w>
-      <w>irt.0p</w>
-      <w>irt.1p</w>
-      <w>irt.2p</w>
-      <w>irt.discrim</w>
-      <w>irt.fa</w>
-      <w>irt.item.diff.rasch</w>
-      <w>irt.person.rasch</w>
-      <w>irt.responses</w>
-      <w>irt.se</w>
-      <w>irt.select</w>
-      <w>irt.stats.like</w>
-      <w>irt.tau</w>
-      <w>irt2latex</w>
-      <w>irunif</w>
-      <w>irwsva.build</w>
-      <w>is</w>
-      <w>is.2x2.correct</w>
-      <w>is.BayesFactor</w>
-      <w>is.Coord</w>
-      <w>is.Date</w>
-      <w>is.Formula</w>
-      <w>is.LLint</w>
-      <w>is.POSIXct</w>
-      <w>is.POSIXlt</w>
-      <w>is.POSIXt</w>
-      <w>is.R</w>
-      <w>is.R6</w>
-      <w>is.R6Class</w>
-      <w>is.SharedData</w>
-      <w>is.Surv</w>
-      <w>is.alicehypercube</w>
-      <w>is.antimagic</w>
-      <w>is.array</w>
-      <w>is.associative</w>
-      <w>is.atomic</w>
-      <w>is.binary</w>
-      <w>is.binary.multiPhylo</w>
-      <w>is.binary.phylo</w>
-      <w>is.binary.tree</w>
-      <w>is.bipartite</w>
-      <w>is.bit</w>
-      <w>is.bitwhich</w>
-      <w>is.bree.correct</w>
-      <w>is.browsable</w>
-      <w>is.call</w>
-      <w>is.centrosymmetric</w>
-      <w>is.character</w>
-      <w>is.chordal</w>
-      <w>is.circulant</w>
-      <w>is.cl_dendrogram</w>
-      <w>is.cl_ensemble</w>
-      <w>is.cl_hard_partition</w>
-      <w>is.cl_hierarchy</w>
-      <w>is.cl_partition</w>
-      <w>is.cl_soft_partition</w>
-      <w>is.compatible</w>
-      <w>is.compatible.bitsplits</w>
-      <w>is.complex</w>
-      <w>is.connected</w>
-      <w>is.count</w>
-      <w>is.dag</w>
-      <w>is.data.frame</w>
-      <w>is.data.table</w>
-      <w>is.date</w>
-      <w>is.debug</w>
-      <w>is.degree.sequence</w>
-      <w>is.dendlist</w>
-      <w>is.dendrogram</w>
-      <w>is.diagonally.correct</w>
-      <w>is.difftime</w>
-      <w>is.dir</w>
-      <w>is.directed</w>
-      <w>is.discrete</w>
-      <w>is.dist</w>
-      <w>is.document_position</w>
-      <w>is.document_range</w>
-      <w>is.double</w>
-      <w>is.duration</w>
-      <w>is.element</w>
-      <w>is.empty.model</w>
-      <w>is.environment</w>
-      <w>is.error</w>
-      <w>is.expression</w>
-      <w>is.facet</w>
-      <w>is.factor</w>
-      <w>is.file</w>
-      <w>is.finite</w>
-      <w>is.flag</w>
-      <w>is.formula</w>
-      <w>is.fractions</w>
-      <w>is.fullrank</w>
-      <w>is.function</w>
-      <w>is.ggplot</w>
-      <w>is.ggproto</w>
-      <w>is.glyphplot</w>
-      <w>is.graphical.degree.sequence</w>
-      <w>is.grob</w>
-      <w>is.grouped_df</w>
-      <w>is.gtable</w>
-      <w>is.hadamard</w>
-      <w>is.hclust</w>
-      <w>is.heterosquare</w>
-      <w>is.hierarchical</w>
-      <w>is.hms</w>
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-      <w>keggGet</w>
-      <w>keggInfo</w>
-      <w>keggLink</w>
-      <w>keggList</w>
-      <w>kegga</w>
-      <w>kegga.DGEExact</w>
-      <w>kegga.DGELRT</w>
-      <w>kegga.MArrayLM</w>
-      <w>kegga.default</w>
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-      <w>kernel</w>
-      <w>kernelFast</w>
-      <w>kernelMatrix</w>
-      <w>kernelMult</w>
-      <w>kernelPol</w>
-      <w>kernelf</w>
-      <w>kernelpls.fit</w>
-      <w>kernlab</w>
-      <w>key</w>
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-      <w>keyname</w>
-      <w>keyorder</w>
-      <w>keys</w>
-      <w>keys.lookup</w>
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-      <w>keysort</w>
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-      <w>kfa</w>
-      <w>kfold</w>
-      <w>kfold_split_grouped</w>
-      <w>kfold_split_random</w>
-      <w>kfold_split_stratified</w>
-      <w>kfoldcv</w>
-      <w>kha</w>
-      <w>khan</w>
-      <w>khanmiss</w>
-      <w>khmaladzize</w>
-      <w>kidney</w>
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-      <w>makeTxDbPackageFromUCSC</w>
-      <w>makeUnique</w>
-      <w>makeUnitVignette</w>
-      <w>makeUsageCollector</w>
-      <w>makeVRangesFromGRanges</w>
-      <w>makeValidParams</w>
-      <w>makeVignetteReference</w>
-      <w>make_</w>
-      <w>make_ansi_style</w>
-      <w>make_bipartite_graph</w>
-      <w>make_call</w>
-      <w>make_chordal_ring</w>
-      <w>make_cluster_plot</w>
-      <w>make_clusters</w>
-      <w>make_date</w>
-      <w>make_datetime</w>
-      <w>make_de_bruijn_graph</w>
-      <w>make_differential_splicing_plot</w>
-      <w>make_difftime</w>
-      <w>make_directed_graph</w>
-      <w>make_eg_to_go_map</w>
-      <w>make_ego_graph</w>
-      <w>make_empty_graph</w>
-      <w>make_full_bipartite_graph</w>
-      <w>make_full_citation_graph</w>
-      <w>make_full_graph</w>
-      <w>make_gene_plot</w>
-      <w>make_go_to_eg_map</w>
-      <w>make_graph</w>
-      <w>make_kautz_graph</w>
-      <w>make_lattice</w>
-      <w>make_line_graph</w>
-      <w>make_option</w>
-      <w>make_ring</w>
-      <w>make_spinner</w>
-      <w>make_star</w>
-      <w>make_style</w>
-      <w>make_tbl</w>
-      <w>make_translations_pkg</w>
-      <w>make_tree</w>
-      <w>make_undirected_graph</w>
-      <w>make_vignette_auxfiles</w>
-      <w>makeconf_path</w>
-      <w>makegrid</w>
-      <w>makemissing</w>
-      <w>makemultdata</w>
-      <w>makepredictcall</w>
-      <w>makespline</w>
-      <w>makevars_site</w>
-      <w>makevars_user</w>
-      <w>mammals</w>
-      <w>manaus</w>
-      <w>mandelbrot</w>
-      <w>mandelbrot_tiles</w>
-      <w>manhattan</w>
-      <w>manifest</w>
-      <w>manipulate</w>
-      <w>manipulatorGetState</w>
-      <w>manipulatorMouseClick</w>
-      <w>manipulatorSetState</w>
-      <w>manova</w>
-      <w>mantel.test</w>
-      <w>mantelhaen.test</w>
-      <w>manual_pal</w>
-      <w>map</w>
-      <w>map.axes</w>
-      <w>map.cities</w>
-      <w>map.clip.poly</w>
-      <w>map.landkreis</w>
-      <w>map.scale</w>
-      <w>map.snps.to.genes</w>
-      <w>map.text</w>
-      <w>map.where</w>
-      <w>map.wrap</w>
-      <w>map.wrap.poly</w>
-      <w>map2</w>
-      <w>map2SpatialLines</w>
-      <w>map2SpatialPolygons</w>
-      <w>map2_chr</w>
-      <w>map2_dbl</w>
-      <w>map2_df</w>
-      <w>map2_dfc</w>
-      <w>map2_dfr</w>
-      <w>map2_int</w>
-      <w>map2_lgl</w>
-      <w>mapCdfName</w>
-      <w>mapClass</w>
-      <w>mapDriveOnWindows</w>
-      <w>mapDriveOnWindows.System</w>
-      <w>mapFromAlignments</w>
-      <w>mapFromTranscripts</w>
-      <w>mapGeneInfo</w>
-      <w>mapGenomeBuilds</w>
-      <w>mapIdentifiers</w>
-      <w>mapIds</w>
-      <w>mapIdsToRanges</w>
-      <w>mapIds_base</w>
-      <w>mapLegendGrob</w>
-      <w>mapLevels</w>
-      <w>mapOrder</w>
-      <w>mapOrgs</w>
-      <w>mapRangesToIds</w>
-      <w>mapSeqlevels</w>
-      <w>mapToAlignments</w>
-      <w>mapToGenome</w>
-      <w>mapToIntervals</w>
-      <w>mapToIntervals.numeric</w>
-      <w>mapToList</w>
-      <w>mapToTranscripts</w>
-      <w>mapValues</w>
-      <w>map_at</w>
-      <w>map_call</w>
-      <w>map_chr</w>
-      <w>map_clusters_to_genes</w>
-      <w>map_data</w>
-      <w>map_dbl</w>
-      <w>map_df</w>
-      <w>map_dfc</w>
-      <w>map_dfr</w>
-      <w>map_if</w>
-      <w>map_int</w>
-      <w>map_lgl</w>
-      <w>mapasp</w>
-      <w>maply</w>
-      <w>mappedLkeys</w>
-      <w>mappedRkeys</w>
-      <w>mappedkeys</w>
-      <w>mapping</w>
-      <w>mapping_color_to_fill</w>
-      <w>mapping_string</w>
-      <w>mapping_swap_x_y</w>
-      <w>mapplot</w>
-      <w>mapply</w>
-      <w>maps</w>
-      <w>maptools</w>
-      <w>mapvalues</w>
-      <w>mar</w>
-      <w>mardia</w>
-      <w>marg.samp</w>
-      <w>margin</w>
-      <w>margin.table</w>
-      <w>margin2table</w>
-      <w>marginal.plot</w>
-      <w>marginalModelPlot</w>
-      <w>marginalModelPlots</w>
-      <w>marginalSECdistr</w>
-      <w>marijuana</w>
-      <w>mark.pathway.by.objects</w>
-      <w>markRenderFunction</w>
-      <w>markTime</w>
-      <w>markdown</w>
-      <w>markdownExtensions</w>
-      <w>markdownHTMLOptions</w>
-      <w>markdownToHTML</w>
-      <w>marker</w>
-      <w>markupSpecs</w>
-      <w>marma</w>
-      <w>marrangeGrob</w>
-      <w>marray</w>
-      <w>maryo</w>
-      <w>mas5</w>
-      <w>mas5.detection</w>
-      <w>mas5calls</w>
-      <w>mas5calls.AffyBatch</w>
-      <w>mas5calls.ProbeSet</w>
-      <w>mask</w>
-      <w>maskFromBSGenome</w>
-      <w>maskGaps</w>
-      <w>maskMotif</w>
-      <w>maskReactiveContext</w>
-      <w>maskeddim</w>
-      <w>maskedncol</w>
-      <w>maskednrow</w>
-      <w>maskedratio</w>
-      <w>maskedwidth</w>
-      <w>masknames</w>
-      <w>masks</w>
-      <w>mass</w>
-      <w>mat.or.vec</w>
-      <w>mat.regress</w>
-      <w>mat.sort</w>
-      <w>mat2tex</w>
-      <w>mat3</w>
-      <w>mat5M3ID</w>
-      <w>mat5Mrand</w>
-      <w>matMaxs</w>
-      <w>matReg</w>
-      <w>matSort</w>
-      <w>matStig</w>
-      <w>matboxplot</w>
-      <w>match</w>
-      <w>match.arg</w>
-      <w>match.call</w>
-      <w>match.fun</w>
-      <w>match.mChoice</w>
-      <w>match.map</w>
-      <w>match.ratetable</w>
-      <w>matchCases</w>
-      <w>matchClasses</w>
-      <w>matchCluster</w>
-      <w>matchCoefs</w>
-      <w>matchControls</w>
-      <w>matchDistribution</w>
-      <w>matchGenes</w>
-      <w>matchIntegerPairs</w>
-      <w>matchIntegerQuads</w>
-      <w>matchLRPatterns</w>
-      <w>matchNamespaces</w>
-      <w>matchPDict</w>
-      <w>matchPWM</w>
-      <w>matchPattern</w>
-      <w>matchProbePair</w>
-      <w>matchSignature</w>
-      <w>match_df</w>
-      <w>match_exact</w>
-      <w>match_ignorecase</w>
-      <w>match_order_by_labels</w>
-      <w>match_order_dendrogram_by_old_order</w>
-      <w>match_partial</w>
-      <w>match_partial_ignorecase</w>
-      <w>match_regexp</w>
-      <w>match_vertices</w>
-      <w>matchcols</w>
-      <w>matches</w>
-      <w>matchprobes</w>
-      <w>matchpt</w>
-      <w>matdensity</w>
-      <w>matern.image.cov</w>
-      <w>matexpo</w>
-      <w>math_format</w>
-      <w>matlines</w>
-      <w>matmax</w>
-      <w>matmin</w>
-      <w>matorder</w>
-      <w>matplot</w>
-      <w>matplotlib</w>
-      <w>matpoints</w>
-      <w>matprod_simple_triplet_matrix</w>
-      <w>matrix</w>
-      <w>matrix2dataFrame</w>
-      <w>matrixClass</w>
-      <w>matrixStats</w>
-      <w>matsort</w>
-      <w>matsqrt</w>
-      <w>matvec</w>
-      <w>matxv</w>
-      <w>mauc</w>
-      <w>mauchly.test</w>
-      <w>max</w>
-      <w>max.bit</w>
-      <w>max.bitwhich</w>
-      <w>max.col</w>
-      <w>max.ri</w>
-      <w>max1</w>
-      <w>maxA</w>
-      <w>maxClique</w>
-      <w>maxDissim</w>
-      <w>maxEmptyRect</w>
-      <w>maxGap</w>
-      <w>maxHypergeo</w>
-      <w>maxMHypergeo</w>
-      <w>maxSE</w>
-      <w>maxScore</w>
-      <w>maxValue</w>
-      <w>maxWavefront</w>
-      <w>maxWeights</w>
-      <w>max_bipartite_match</w>
-      <w>max_cardinality</w>
-      <w>max_chroma</w>
-      <w>max_chroma_table</w>
-      <w>max_cliques</w>
-      <w>max_cohesion</w>
-      <w>max_depth</w>
-      <w>max_flow</w>
-      <w>max_height</w>
-      <w>max_width</w>
-      <w>maxcohesion</w>
-      <w>maximal.cliques</w>
-      <w>maximal.cliques.count</w>
-      <w>maximal.independent.vertex.sets</w>
-      <w>maximal_ivs</w>
-      <w>maximizeCcf</w>
-      <w>maximizeInterpolant</w>
-      <w>maximizeQuadratic</w>
-      <w>maximize_correlation</w>
-      <w>maximum.bipartite.matching</w>
-      <w>maximum.cardinality.search</w>
-      <w>maximumCycleRatio</w>
-      <w>maximump</w>
-      <w>maxresiduals</w>
-      <w>mayonnaise</w>
-      <w>mbarclPanel</w>
-      <w>mbarclpl</w>
-      <w>mc</w>
-      <w>mc.reset.stream</w>
-      <w>mcMap</w>
-      <w>mcPlot</w>
-      <w>mcPlots</w>
-      <w>mca</w>
-      <w>mcaffinity</w>
-      <w>mcat</w>
-      <w>mcc</w>
-      <w>mccollect</w>
-      <w>mcconwaysims.test</w>
-      <w>mclapply</w>
-      <w>mclust</w>
-      <w>mclust.options</w>
-      <w>mclust1Dplot</w>
-      <w>mclust2Dplot</w>
-      <w>mclustBIC</w>
-      <w>mclustBICupdate</w>
-      <w>mclustBootstrapLRT</w>
-      <w>mclustICL</w>
-      <w>mclustLoglik</w>
-      <w>mclustModel</w>
-      <w>mclustModelNames</w>
-      <w>mclustVariance</w>
-      <w>mclusterSim</w>
-      <w>mcmapply</w>
-      <w>mcmc</w>
-      <w>mcmc.list</w>
-      <w>mcmc.popsize</w>
-      <w>mcmcUpgrade</w>
-      <w>mcnemar.test</w>
-      <w>mcolAsRleList</w>
-      <w>mcols</w>
-      <w>mcpar</w>
-      <w>mcparallel</w>
-      <w>mcse_loo</w>
-      <w>mcyc</w>
-      <w>mcycle</w>
-      <w>md.plot</w>
-      <w>md4</w>
-      <w>md5</w>
-      <w>md5sum</w>
-      <w>md_document</w>
-      <w>mday</w>
-      <w>mdb.get</w>
-      <w>mdplot</w>
-      <w>mdply</w>
-      <w>mdsPlot</w>
-      <w>mdy</w>
-      <w>mdy_h</w>
-      <w>mdy_hm</w>
-      <w>mdy_hms</w>
-      <w>me</w>
-      <w>me.weighted</w>
-      <w>meE</w>
-      <w>meEEE</w>
-      <w>meEEI</w>
-      <w>meEEV</w>
-      <w>meEII</w>
-      <w>meEVE</w>
-      <w>meEVI</w>
-      <w>meEVV</w>
-      <w>meV</w>
-      <w>meVEE</w>
-      <w>meVEI</w>
-      <w>meVEV</w>
-      <w>meVII</w>
-      <w>meVVE</w>
-      <w>meVVI</w>
-      <w>meVVV</w>
-      <w>meX</w>
-      <w>meXII</w>
-      <w>meXXI</w>
-      <w>meXXX</w>
-      <w>mean</w>
-      <w>mean.Date</w>
-      <w>mean.DelayedArray</w>
-      <w>mean.POSIXct</w>
-      <w>mean.POSIXlt</w>
-      <w>mean.Rle</w>
-      <w>mean.default</w>
-      <w>mean.difftime</w>
-      <w>mean.na</w>
-      <w>mean0</w>
-      <w>mean2</w>
-      <w>meanDistance</w>
-      <w>meanFNCHypergeo</w>
-      <w>meanInRegions</w>
-      <w>meanMFNCHypergeo</w>
-      <w>meanMWNCHypergeo</w>
-      <w>meanNeighbors</w>
-      <w>meanOver</w>
-      <w>meanSdPlot</w>
-      <w>meanT</w>
-      <w>meanWNCHypergeo</w>
-      <w>meanX</w>
-      <w>mean_R_NX</w>
-      <w>mean_ci</w>
-      <w>mean_cl_boot</w>
-      <w>mean_cl_normal</w>
-      <w>mean_distance</w>
-      <w>mean_range</w>
-      <w>mean_sd</w>
-      <w>mean_sdl</w>
-      <w>mean_se</w>
-      <w>mean_se_</w>
-      <w>meanabsdev</w>
-      <w>meanp</w>
-      <w>meanval.digamma</w>
-      <w>meanvar</w>
-      <w>meanz</w>
-      <w>measurement</w>
-      <w>measurement.error</w>
-      <w>measurementError</w>
-      <w>medflies</w>
-      <w>median</w>
-      <w>median.Rle</w>
-      <w>median.default</w>
-      <w>median.zoo</w>
-      <w>medianBackground</w>
-      <w>medianNormalise</w>
-      <w>median_hilow</w>
-      <w>median_iqr</w>
-      <w>median_mad</w>
-      <w>median_range</w>
-      <w>medianpolish</w>
-      <w>mediate</w>
-      <w>mediate.diagram</w>
-      <w>medpolish</w>
-      <w>medvPanel</w>
-      <w>medvpl</w>
-      <w>melanoma</w>
-      <w>melon</w>
-      <w>melt</w>
-      <w>melt.data.table</w>
-      <w>melt_csv</w>
-      <w>melt_csv2</w>
-      <w>melt_csv2_chunked</w>
-      <w>melt_csv_chunked</w>
-      <w>melt_delim</w>
-      <w>melt_delim_chunked</w>
-      <w>melt_fwf</w>
-      <w>melt_table</w>
-      <w>melt_table2</w>
-      <w>melt_tsv</w>
-      <w>melt_tsv_chunked</w>
-      <w>mem.limits</w>
-      <w>memCompress</w>
-      <w>memDecompress</w>
-      <w>members</w>
-      <w>membersExpr</w>
-      <w>membersScore</w>
-      <w>membership</w>
-      <w>memoise</w>
-      <w>memoize</w>
-      <w>memory.limit</w>
-      <w>memory.profile</w>
-      <w>memory.size</w>
-      <w>memoryCache</w>
-      <w>menarche</w>
-      <w>mendoapply</w>
-      <w>menu</w>
-      <w>menuItem</w>
-      <w>menuItemOutput</w>
-      <w>menuSubItem</w>
-      <w>merge</w>
-      <w>merge.AffyBatch</w>
-      <w>merge.EList</w>
-      <w>merge.EListRaw</w>
-      <w>merge.MAList</w>
-      <w>merge.RGList</w>
-      <w>merge.data.frame</w>
-      <w>merge.default</w>
-      <w>merge.list</w>
-      <w>merge.zoo</w>
-      <w>merge2Clusters</w>
-      <w>mergeBam</w>
-      <w>mergeBamByFactor</w>
-      <w>mergeByCommonTails</w>
-      <w>mergeByOverlaps</w>
-      <w>mergeCAGEsets</w>
-      <w>mergeCells</w>
-      <w>mergeIUPACLetters</w>
-      <w>mergeIntervals</w>
-      <w>mergeIntervals.numeric</w>
-      <w>mergeMethods</w>
-      <w>mergeProbeDesigns</w>
-      <w>mergeProbeDesigns2</w>
-      <w>mergeRegions</w>
-      <w>mergeReplicates</w>
-      <w>mergeSamples</w>
-      <w>mergeScansRG</w>
-      <w>mergeToNamespaceAndExport</w>
-      <w>mergeWindows</w>
-      <w>merge_base</w>
-      <w>merge_coords</w>
-      <w>merge_element</w>
-      <w>merge_two_expfiles</w>
-      <w>mergedTrellisLegendGrob</w>
-      <w>merged_ewce</w>
-      <w>mergenormCBI</w>
-      <w>mergenormals</w>
-      <w>mergeorder</w>
-      <w>mergeparameters</w>
-      <w>merges</w>
-      <w>mergesort</w>
-      <w>mergesortorder</w>
-      <w>mesh.dcircle</w>
-      <w>mesh.diff</w>
-      <w>mesh.drectangle</w>
-      <w>mesh.dsphere</w>
-      <w>mesh.hunif</w>
-      <w>mesh.intersect</w>
-      <w>mesh.union</w>
-      <w>message</w>
-      <w>messageItem</w>
-      <w>message_for_status</w>
-      <w>messagef</w>
-      <w>meta</w>
-      <w>metaNameUndo</w>
-      <w>metaTemplate</w>
-      <w>metadata</w>
-      <w>metap</w>
-      <w>method.skeleton</w>
-      <w>methodSignatureMatrix</w>
-      <w>methods</w>
-      <w>methodsInheritedFrom</w>
-      <w>methodsInheritedFrom.Rdoc</w>
-      <w>methodsPackageMetaName</w>
-      <w>methylated</w>
-      <w>methylated.N</w>
-      <w>methylationCall</w>
-      <w>methylumIDAT</w>
-      <w>methylumIDATepic</w>
-      <w>methylumi</w>
-      <w>methylumi.bgcorr</w>
-      <w>methylumi.diagnostics</w>
-      <w>methylumiCSV</w>
-      <w>methylumiR</w>
-      <w>metrics</w>
-      <w>metrop</w>
-      <w>meuse</w>
-      <w>meuse.area</w>
-      <w>meuse.grid</w>
-      <w>meuse.grid_ll</w>
-      <w>meuse.riv</w>
-      <w>mfrow</w>
-      <w>mgEdgeData</w>
-      <w>mgEdgeDataDefaults</w>
-      <w>mgcv</w>
-      <w>mgedist</w>
-      <w>mgeneSim</w>
-      <w>mget</w>
-      <w>mgi_synonym_data</w>
-      <w>mglmLevenberg</w>
-      <w>mglmOneGroup</w>
-      <w>mglmOneWay</w>
-      <w>mgoSim</w>
-      <w>mgp.axis</w>
-      <w>mgp.axis.labels</w>
-      <w>mgus</w>
-      <w>mgus2</w>
-      <w>mhgr</w>
-      <w>mic</w>
-      <w>michelson</w>
-      <w>microRNAs</w>
-      <w>microseconds</w>
-      <w>mid</w>
-      <w>midnightStandard</w>
-      <w>midnightStandard2</w>
-      <w>midwest</w>
-      <w>milk</w>
-      <w>milliseconds</w>
-      <w>mime</w>
-      <w>mimeTypeExtensions</w>
-      <w>mime_part</w>
-      <w>mimemap</w>
-      <w>min</w>
-      <w>min.bit</w>
-      <w>min.bitwhich</w>
-      <w>min.ri</w>
-      <w>min0</w>
-      <w>minCut</w>
-      <w>minDegreeOrdering</w>
-      <w>minDiss</w>
-      <w>minHypergeo</w>
-      <w>minMHypergeo</w>
-      <w>minScore</w>
-      <w>minValue</w>
-      <w>minWeights</w>
-      <w>min_cut</w>
-      <w>min_depth</w>
-      <w>min_rank</w>
-      <w>min_separators</w>
-      <w>min_st_separators</w>
-      <w>mine</w>
-      <w>minfi</w>
-      <w>minfiData</w>
-      <w>minfiQC</w>
-      <w>mini.roots</w>
-      <w>miniACC</w>
-      <w>minify</w>
-      <w>minimal.st.separators</w>
-      <w>minimax.crit</w>
-      <w>minimum.size.separators</w>
-      <w>minimum.spanning.tree</w>
-      <w>minimumCycleRatio</w>
-      <w>minimump</w>
-      <w>minitri</w>
-      <w>minkowski</w>
-      <w>minmax</w>
-      <w>minn38</w>
-      <w>minor.tick</w>
-      <w>minqa</w>
-      <w>minsize</w>
-      <w>minute</w>
-      <w>minutes</w>
-      <w>mirror2html</w>
-      <w>mismatch</w>
-      <w>mismatchSummary</w>
-      <w>mismatchTable</w>
-      <w>missMethyl</w>
-      <w>missing</w>
-      <w>missingArg</w>
-      <w>missingCh</w>
-      <w>missing_arg</w>
-      <w>missing_s3</w>
-      <w>missingdata</w>
-      <w>mixColor1Ramps</w>
-      <w>mixColor2Ramps</w>
-      <w>mixColor3Ramps</w>
-      <w>mixColorRamps</w>
-      <w>mixcolor</w>
-      <w>mixdens</w>
-      <w>mixed.cor</w>
-      <w>mixedClusters</w>
-      <w>mixedCor</w>
-      <w>mixedFontLabel</w>
-      <w>mixedModel2</w>
-      <w>mixedModel2Fit</w>
-      <w>mixedOverlaps</w>
-      <w>mixedorder</w>
-      <w>mixedsort</w>
-      <w>mixpredictive</w>
-      <w>mixtools</w>
-      <w>mixture</w>
-      <w>mkAllStrings</w>
-      <w>mkRespMod</w>
-      <w>mkScalar</w>
-      <w>mkdirs</w>
-      <w>mkdirs.default</w>
-      <w>mkoptions</w>
-      <w>mlArrange</w>
-      <w>mlPlot</w>
-      <w>mldat</w>
-      <w>mle</w>
-      <w>mle.nomean</w>
-      <w>mle.nomean.spam</w>
-      <w>mle.spam</w>
-      <w>mledist</w>
-      <w>mlike</w>
-      <w>mlistMetaName</w>
-      <w>mlogLoss</w>
-      <w>mlply</w>
-      <w>mlr</w>
-      <w>mlsl</w>
-      <w>mltdrb</w>
-      <w>mltt.plot</w>
-      <w>mm</w>
-      <w>mm7.ensGene.LENGTH</w>
-      <w>mm7.geneSymbol.LENGTH</w>
-      <w>mm7.geneid.LENGTH</w>
-      <w>mm7.genscan.LENGTH</w>
-      <w>mm7.knownGene.LENGTH</w>
-      <w>mm7.refGene.LENGTH</w>
-      <w>mm7.sgpGene.LENGTH</w>
-      <w>mm7.xenoRefGene.LENGTH</w>
-      <w>mm8.ccdsGene.LENGTH</w>
-      <w>mm8.ensGene.LENGTH</w>
-      <w>mm8.geneSymbol.LENGTH</w>
-      <w>mm8.geneid.LENGTH</w>
-      <w>mm8.genscan.LENGTH</w>
-      <w>mm8.knownGene.LENGTH</w>
-      <w>mm8.nscanGene.LENGTH</w>
-      <w>mm8.refGene.LENGTH</w>
-      <w>mm8.sgpGene.LENGTH</w>
-      <w>mm8.sibGene.LENGTH</w>
-      <w>mm8.xenoRefGene.LENGTH</w>
-      <w>mm9.acembly.LENGTH</w>
-      <w>mm9.ccdsGene.LENGTH</w>
-      <w>mm9.ensGene.LENGTH</w>
-      <w>mm9.exoniphy.LENGTH</w>
-      <w>mm9.geneSymbol.LENGTH</w>
-      <w>mm9.geneid.LENGTH</w>
-      <w>mm9.genscan.LENGTH</w>
-      <w>mm9.knownGene.LENGTH</w>
-      <w>mm9.nscanGene.LENGTH</w>
-      <w>mm9.refGene.LENGTH</w>
-      <w>mm9.sgpGene.LENGTH</w>
-      <w>mm9.xenoRefGene.LENGTH</w>
-      <w>mma</w>
-      <w>mmdstats</w>
-      <w>mmedist</w>
-      <w>mmindex</w>
-      <w>mmp</w>
-      <w>mmps</w>
-      <w>mmsamp</w>
-      <w>mnLogLoss</w>
-      <w>mnnCorrect</w>
-      <w>mnormt</w>
-      <w>mnsl</w>
-      <w>mnsl2hex</w>
-      <w>mnsl2hvc</w>
-      <w>mnsl_hues</w>
-      <w>moby</w>
-      <w>moby_sample</w>
-      <w>mock</w>
-      <w>mod</w>
-      <w>mod.matrix</w>
-      <w>modal</w>
-      <w>modalButton</w>
-      <w>modalDialog</w>
-      <w>mode</w>
-      <w>modeFNCHypergeo</w>
-      <w>modeSECdistr</w>
-      <w>modeWNCHypergeo</w>
-      <w>model.Matrix</w>
-      <w>model.design</w>
-      <w>model.extract</w>
-      <w>model.frame</w>
-      <w>model.frame.default</w>
-      <w>model.guess</w>
-      <w>model.matrix</w>
-      <w>model.matrix.default</w>
-      <w>model.matrix.gam</w>
-      <w>model.matrix.lm</w>
-      <w>model.offset</w>
-      <w>model.part</w>
-      <w>model.response</w>
-      <w>model.tables</w>
-      <w>model.weights</w>
-      <w>model.xexact</w>
-      <w>model2restrictionMatrix</w>
-      <w>model2restrictionMatrix.lm</w>
-      <w>model2restrictionMatrix.mer</w>
-      <w>model2restrictionMatrix.merMod</w>
-      <w>modelCor</w>
-      <w>modelLookup</w>
-      <w>modelMatrix</w>
-      <w>modelMatrixMeth</w>
-      <w>modelPar</w>
-      <w>modelVar</w>
-      <w>model_beta_label</w>
-      <w>model_beta_variables</w>
-      <w>model_response_variables</w>
-      <w>modelsearch</w>
-      <w>modeltools</w>
-      <w>moderate.diagram</w>
-      <w>modifications</w>
-      <w>modify</w>
-      <w>modifyBaseFont</w>
-      <w>modifyList</w>
-      <w>modifyRange</w>
-      <w>modifyWeights</w>
-      <w>modify_at</w>
-      <w>modify_depth</w>
-      <w>modify_if</w>
-      <w>modify_url</w>
-      <w>modularity</w>
-      <w>modularity_matrix</w>
-      <w>modulelist</w>
-      <w>moduleload</w>
-      <w>modules</w>
-      <w>modulus_trans</w>
-      <w>mold</w>
-      <w>moment</w>
-      <w>moments</w>
-      <w>momentsMFNCHypergeo</w>
-      <w>momentsMWNCHypergeo</w>
-      <w>monDom1.genscan.LENGTH</w>
-      <w>monDom4.ensGene.LENGTH</w>
-      <w>monDom4.geneSymbol.LENGTH</w>
-      <w>monDom4.genscan.LENGTH</w>
-      <w>monDom4.nscanGene.LENGTH</w>
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-      <w>monDom4.xenoRefGene.LENGTH</w>
-      <w>monDom5.ensGene.LENGTH</w>
-      <w>monDom5.geneSymbol.LENGTH</w>
-      <w>monDom5.genscan.LENGTH</w>
-      <w>monDom5.nscanGene.LENGTH</w>
-      <w>monDom5.refGene.LENGTH</w>
-      <w>monDom5.xenoRefGene.LENGTH</w>
-      <w>mona</w>
-      <w>moneydemand</w>
-      <w>monic</w>
-      <w>monitor</w>
-      <w>mono.con</w>
-      <w>monograph_group</w>
-      <w>monoreg</w>
-      <w>monotone</w>
-      <w>month</w>
-      <w>month.abb</w>
-      <w>month.name</w>
-      <w>monthDays</w>
-      <w>monthlyRolling</w>
-      <w>monthplot</w>
-      <w>months</w>
-      <w>months.Date</w>
-      <w>months.POSIXt</w>
-      <w>mood.test</w>
-      <w>more</w>
-      <w>more.Verbose</w>
-      <w>mori2006</w>
-      <w>morley</w>
-      <w>morph</w>
-      <w>morph.identity</w>
-      <w>morph.metrop</w>
-      <w>mortality</w>
-      <w>morths</w>
-      <w>mosaic</w>
-      <w>mosaicplot</w>
-      <w>mostEdges</w>
-      <w>motifDiffEnrichment</w>
-      <w>motifEcdf</w>
-      <w>motifEnrichment</w>
-      <w>motifIC</w>
-      <w>motifRankingForGroup</w>
-      <w>motifRankingForSequence</w>
-      <w>motifScores</w>
-      <w>motifSimilarity</w>
-      <w>motifs</w>
-      <w>motor</w>
-      <w>motors</w>
-      <w>mourning</w>
-      <w>mouse.table</w>
-      <w>mouse_to_human_homologs</w>
-      <w>mout</w>
-      <w>moveInSearchPath</w>
-      <w>moveInSearchPath.default</w>
-      <w>moveToGrob</w>
-      <w>movingAverageByCol</w>
-      <w>movingFun</w>
-      <w>mpager</w>
-      <w>mpg</w>
-      <w>mpl</w>
-      <w>mprint</w>
-      <w>mprintf</w>
-      <w>mptable</w>
-      <w>mrca</w>
-      <w>mrequire</w>
-      <w>mrlm</w>
-      <w>mrlplot</w>
-      <w>mroast</w>
-      <w>mroast.DGEList</w>
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-      <w>ms</w>
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-      <w>mse</w>
-      <w>mseqnames</w>
-      <w>mshow</w>
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-      <w>msn.mle</w>
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-      <w>msq</w>
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-      <w>mssd</w>
-      <w>mst</w>
-      <w>mst.mple</w>
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-      <w>mstr</w>
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-      <w>mt.plot</w>
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-      <w>mt.sample.rawp</w>
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-      <w>mt.teststat</w>
-      <w>mt.teststat.num.denum</w>
-      <w>mtcars</w>
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-      <w>multLines</w>
-      <w>multWendlandGrid</w>
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-      <w>multi2di.phylo</w>
-      <w>multiClassSummary</w>
-      <w>multiTextGatherer</w>
-      <w>multi_add</w>
-      <w>multi_cancel</w>
-      <w>multi_fdset</w>
-      <w>multi_list</w>
-      <w>multi_run</w>
-      <w>multi_set</w>
-      <w>multiassign</w>
-      <w>multicore</w>
-      <w>multicoreWorkers</w>
-      <w>multidensity</w>
-      <w>multiecdf</w>
-      <w>multiedit</w>
-      <w>multigroup</w>
-      <w>multiinformation</w>
-      <w>multilevel.community</w>
-      <w>multilevel.reliability</w>
-      <w>multiloess</w>
-      <w>multinom</w>
-      <w>multinomial</w>
-      <w>multipleClasses</w>
-      <w>multiplot</w>
-      <w>multiply_by</w>
-      <w>multiply_by_matrix</w>
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-      <w>multivari</w>
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-      <w>muscle</w>
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-      <w>mvn</w>
-      <w>mvn.lvm</w>
-      <w>mvn2plot</w>
-      <w>mvnX</w>
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-      <w>mvr</w>
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-      <w>mvrnorm</w>
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-      <w>mvtnorm</w>
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-      <w>my_pubkey</w>
-      <w>myd</w>
-      <w>myeloid</w>
-      <w>mypredict.lm</w>
-      <w>myscreeplot</w>
-      <w>mysqlBuildTableDefinition</w>
-      <w>mysqlClientLibraryVersions</w>
-      <w>mysqlHasDefault</w>
-      <w>mz</w>
-      <w>n</w>
-      <w>n.code</w>
-      <w>n.plot</w>
-      <w>n2mfrow</w>
-      <w>n2w</w>
-      <w>nChrom</w>
-      <w>nCm</w>
-      <w>nFilter</w>
-      <w>nFm</w>
-      <w>nLnode</w>
-      <w>nM2par</w>
-      <w>nMDS</w>
-      <w>nMclustParams</w>
-      <w>nObservations</w>
-      <w>nPairs</w>
-      <w>nRnode</w>
-      <w>nSV</w>
-      <w>nVarParams</w>
-      <w>n_distinct</w>
-      <w>n_fields</w>
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-      <w>na.delete</w>
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-      <w>naiveRangeMapper</w>
-      <w>name</w>
-      <w>name_rows</w>
-      <w>namedList</w>
-      <w>names</w>
-      <w>names.Object</w>
-      <w>names.Options</w>
-      <w>names.POSIXlt</w>
-      <w>names.XMLNode</w>
-      <w>names0</w>
-      <w>names2</w>
-      <w>namespaceExport</w>
-      <w>namespaceImport</w>
-      <w>namespaceImportClasses</w>
-      <w>namespaceImportFrom</w>
-      <w>namespaceImportMethods</w>
-      <w>nanes</w>
-      <w>nanet</w>
-      <w>nanoseconds</w>
-      <w>naplot</w>
-      <w>napredict</w>
-      <w>napredict.delete</w>
-      <w>naprint</w>
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-      <w>naprint.keep</w>
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-      <w>naresid.delete</w>
-      <w>naresid.keep</w>
-      <w>nargs</w>
-      <w>narrow</w>
-      <w>nasa</w>
-      <w>nasen</w>
-      <w>nastats</w>
-      <w>naten</w>
-      <w>native_american</w>
-      <w>native_encode</w>
-      <w>natstobits</w>
-      <w>navbarMenu</w>
-      <w>navbarPage</w>
-      <w>navbar_html</w>
-      <w>navbar_links_html</w>
-      <w>navigateToFile</w>
-      <w>navlistPanel</w>
-      <w>nb</w>
-      <w>nbBag</w>
-      <w>nbBeadsFilter</w>
-      <w>nbFuncs</w>
-      <w>nbSBF</w>
-      <w>nbands</w>
-      <w>nbinomDeviance</w>
-      <w>nbinomLRT</w>
-      <w>nbinomUnitDeviance</w>
-      <w>nbinomWaldTest</w>
-      <w>nbins</w>
-      <w>nbrOfOptions</w>
-      <w>nbrOfOptions.Options</w>
-      <w>nbrOfWorkers</w>
-      <w>nbtest</w>
-      <w>ncbi_snp_query</w>
-      <w>ncbi_snp_query2</w>
-      <w>ncbi_snp_summary</w>
-      <w>ncell</w>
-      <w>nchain</w>
-      <w>nchar</w>
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-      <w>nchar_sgr</w>
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-      <w>nclass.Sturges</w>
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-      <w>ncol</w>
-      <w>ncoord</w>
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-      <w>ncvTest</w>
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-      <w>near</w>
-      <w>nearPD</w>
-      <w>nearPoints</w>
-      <w>nearZeroVar</w>
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-      <w>nearest.dist</w>
-      <w>nearestPointOnLine</w>
-      <w>nearestPointOnSegment</w>
-      <w>nearestReftoX</w>
-      <w>nearestTSS</w>
-      <w>nec</w>
-      <w>nedit</w>
-      <w>neditAt</w>
-      <w>neditEndingAt</w>
-      <w>neditStartingAt</w>
-      <w>need</w>
-      <w>needUpdate</w>
-      <w>needs_compile</w>
-      <w>needwunsQS</w>
-      <w>neg.bin</w>
-      <w>neg2loglikelihood</w>
-      <w>neg2loglikelihood.spam</w>
-      <w>negPredValue</w>
-      <w>negate</w>
-      <w>negative.binomial</w>
-      <w>negbin</w>
-      <w>negctls</w>
-      <w>negctls.stderr</w>
-      <w>negexp.SSival</w>
-      <w>neginc</w>
-      <w>negnorm</w>
-      <w>neighborhood</w>
-      <w>neighborhood.size</w>
-      <w>neighbors</w>
-      <w>nelder</w>
-      <w>neldermead</w>
-      <w>neo</w>
-      <w>neqc</w>
-      <w>nest</w>
-      <w>nest_</w>
-      <w>nested.corr</w>
-      <w>nestedListing</w>
-      <w>nesting</w>
-      <w>nesting_</w>
-      <w>netToAxt</w>
-      <w>netplot</w>
-      <w>neuro</w>
-      <w>new</w>
-      <w>new.env</w>
-      <w>new.name</w>
-      <w>new.packages</w>
-      <w>new2</w>
-      <w>new2old.phylo</w>
-      <w>newBasic</w>
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-      <w>parfix</w>
-      <w>parlabels</w>
-      <w>parpos</w>
-      <w>pars</w>
-      <w>parse</w>
-      <w>parse.GString</w>
-      <w>parse.SmartComments</w>
-      <w>parse.constraints</w>
-      <w>parse.default</w>
-      <w>parse.grid.list</w>
-      <w>parse2GRanges</w>
-      <w>parseArgs</w>
-      <w>parseArgsForAes</w>
-      <w>parseArgsForNonAes</w>
-      <w>parseDTD</w>
-      <w>parseDebian</w>
-      <w>parseDebian.System</w>
-      <w>parseDesc</w>
-      <w>parseGEO</w>
-      <w>parseHTTPHeader</w>
-      <w>parseLatex</w>
-      <w>parseNamespaceFile</w>
-      <w>parsePackageCitation</w>
-      <w>parseQueryString</w>
-      <w>parseRepos</w>
-      <w>parseSpecialNames</w>
-      <w>parseURI</w>
-      <w>parseWIG</w>
-      <w>parseXMLAndAdd</w>
-      <w>parse_1usage_text</w>
-      <w>parse_Rd</w>
-      <w>parse_Rdname</w>
-      <w>parse_Rdpiece</w>
-      <w>parse_Rdtext</w>
-      <w>parse_all</w>
-      <w>parse_args</w>
-      <w>parse_args2</w>
-      <w>parse_character</w>
-      <w>parse_check</w>
-      <w>parse_check_url</w>
-      <w>parse_date</w>
-      <w>parse_date_time</w>
-      <w>parse_date_time2</w>
-      <w>parse_datetime</w>
-      <w>parse_deps</w>
-      <w>parse_double</w>
-      <w>parse_env_subset</w>
-      <w>parse_factor</w>
-      <w>parse_format</w>
-      <w>parse_github_repo_spec</w>
-      <w>parse_github_url</w>
-      <w>parse_guess</w>
-      <w>parse_headers</w>
-      <w>parse_headers_list</w>
-      <w>parse_hm</w>
-      <w>parse_hms</w>
-      <w>parse_html_notebook</w>
-      <w>parse_http_date</w>
-      <w>parse_integer</w>
-      <w>parse_json</w>
-      <w>parse_logical</w>
-      <w>parse_media</w>
-      <w>parse_multipart</w>
-      <w>parse_ns_file</w>
-      <w>parse_number</w>
-      <w>parse_only</w>
-      <w>parse_packages</w>
-      <w>parse_pairlist</w>
-      <w>parse_repo_spec</w>
-      <w>parse_time</w>
-      <w>parse_url</w>
-      <w>parse_usage_text</w>
-      <w>parse_vector</w>
-      <w>parsed_content</w>
-      <w>parsedesign</w>
-      <w>partconv</w>
-      <w>partial</w>
-      <w>partial.r</w>
-      <w>partial_bundle</w>
-      <w>partial_eigen</w>
-      <w>partial_frame</w>
-      <w>partialcor</w>
-      <w>partition.matrix</w>
-      <w>partition.vector</w>
-      <w>partition_leaves</w>
-      <w>partuniq</w>
-      <w>passwordInput</w>
-      <w>paste</w>
-      <w>paste.vec</w>
-      <w>paste0</w>
-      <w>pasteCols</w>
-      <w>pasteFit</w>
-      <w>pasteTree</w>
-      <w>pasteTree.FileListTree</w>
-      <w>pat_asciidoc</w>
-      <w>pat_brew</w>
-      <w>pat_html</w>
-      <w>pat_md</w>
-      <w>pat_rnw</w>
-      <w>pat_rst</w>
-      <w>pat_tex</w>
-      <w>pat_textile</w>
-      <w>patchCode</w>
-      <w>patchCode.default</w>
-      <w>patent</w>
-      <w>path</w>
-      <w>path.expand</w>
-      <w>path.length.hist</w>
-      <w>path.package</w>
-      <w>path.rpart</w>
-      <w>pathGrob</w>
-      <w>pathListing</w>
-      <w>pathWeights</w>
-      <w>path_abs</w>
-      <w>path_common</w>
-      <w>path_dir</w>
-      <w>path_expand</w>
-      <w>path_expand_r</w>
-      <w>path_ext</w>
-      <w>path_ext_remove</w>
-      <w>path_ext_set</w>
-      <w>path_file</w>
-      <w>path_filter</w>
-      <w>path_has_parent</w>
-      <w>path_home</w>
-      <w>path_home_r</w>
-      <w>path_join</w>
-      <w>path_norm</w>
-      <w>path_package</w>
-      <w>path_real</w>
-      <w>path_rel</w>
-      <w>path_sanitize</w>
-      <w>path_split</w>
-      <w>path_temp</w>
-      <w>path_tidy</w>
-      <w>path_wd</w>
-      <w>pattern</w>
-      <w>patternFrequency</w>
-      <w>paulsen</w>
-      <w>pause</w>
-      <w>paxis3d</w>
-      <w>pbClose</w>
-      <w>pbCreate</w>
-      <w>pbStep</w>
-      <w>pbapply</w>
-      <w>pbc</w>
-      <w>pbeta</w>
-      <w>pbgyr</w>
-      <w>pbinom</w>
-      <w>pbirthday</w>
-      <w>pbkrtest</w>
-      <w>pblapply</w>
-      <w>pbmapply</w>
-      <w>pbmc</w>
-      <w>pbmc_small</w>
-      <w>pboptions</w>
-      <w>pbreplicate</w>
-      <w>pbsapply</w>
-      <w>pbtypes</w>
-      <w>pbvalog</w>
-      <w>pbvamix</w>
-      <w>pbvaneglog</w>
-      <w>pbvbilog</w>
-      <w>pbvct</w>
-      <w>pbvevd</w>
-      <w>pbvhr</w>
-      <w>pbvlog</w>
-      <w>pbvnegbilog</w>
-      <w>pbvneglog</w>
-      <w>pc</w>
-      <w>pc1</w>
-      <w>pca</w>
-      <w>pca.distances</w>
-      <w>pca.scoreplot</w>
-      <w>pcaNNet</w>
-      <w>pcaPP</w>
-      <w>pcauchy</w>
-      <w>pchisq</w>
-      <w>pcls</w>
-      <w>pclust</w>
-      <w>pclust_family</w>
-      <w>pclust_object</w>
-      <w>pcoa</w>
-      <w>pcompare</w>
-      <w>pcompareRecursively</w>
-      <w>pcor</w>
-      <w>pcor0</w>
-      <w>pcouted</w>
-      <w>pcoverageByTranscript</w>
-      <w>pcr</w>
-      <w>pcramer</w>
-      <w>pcre_config</w>
-      <w>pcv</w>
-      <w>pd.solve</w>
-      <w>pdBlocked</w>
-      <w>pdCompSymm</w>
-      <w>pdConstruct</w>
-      <w>pdDiag</w>
-      <w>pdFactor</w>
-      <w>pdIdent</w>
-      <w>pdIdnot</w>
-      <w>pdLogChol</w>
-      <w>pdMat</w>
-      <w>pdMatrix</w>
-      <w>pdNatural</w>
-      <w>pdSymm</w>
-      <w>pdTens</w>
-      <w>pdf</w>
-      <w>pdf.do</w>
-      <w>pdf.end</w>
-      <w>pdf.latex</w>
-      <w>pdf.options</w>
-      <w>pdfFonts</w>
-      <w>pdf_document</w>
-      <w>pdfclustCBI</w>
-      <w>pdfconvert</w>
-      <w>pdflatex</w>
-      <w>pdiscrete</w>
-      <w>peakHeatmap</w>
-      <w>peaks</w>
-      <w>peas</w>
-      <w>peek_vars</w>
-      <w>pen.edf</w>
-      <w>penalise</w>
-      <w>penny</w>
-      <w>pension</w>
-      <w>peptides</w>
-      <w>percent</w>
-      <w>percent_format</w>
-      <w>percent_rank</w>
-      <w>perfectcube5</w>
-      <w>perfectcube6</w>
-      <w>performance</w>
-      <w>period</w>
-      <w>period_to_seconds</w>
-      <w>periodicSpline</w>
-      <w>periodicallyRolling</w>
-      <w>periods</w>
-      <w>perm</w>
-      <w>perm.rowscols</w>
-      <w>permSumStats</w>
-      <w>permSumStats.all</w>
-      <w>permTest</w>
-      <w>permn</w>
-      <w>permp</w>
-      <w>permutation</w>
-      <w>permutation.spam</w>
-      <w>permutations</w>
-      <w>permute</w>
-      <w>permute.vertices</w>
-      <w>person</w>
-      <w>personList</w>
-      <w>persp</w>
-      <w>perspx</w>
-      <w>petMar1.xenoRefGene.LENGTH</w>
-      <w>petest</w>
-      <w>petrol</w>
-      <w>pexp</w>
-      <w>pextreme</w>
-      <w>pf</w>
-      <w>pfilter</w>
-      <w>pfrechet</w>
-      <w>pgamma</w>
-      <w>pgap</w>
-      <w>pgeom</w>
-      <w>pgev</w>
-      <w>pgpd</w>
-      <w>pgumbel</w>
-      <w>phalfnorm</w>
-      <w>phead</w>
-      <w>pheatmap</w>
-      <w>phenoData</w>
-      <w>phenoModel</w>
-      <w>phenotype</w>
-      <w>phenotypeColor</w>
-      <w>phenotypes</w>
-      <w>phenotypes_byid</w>
-      <w>phi</w>
-      <w>phi.demo</w>
-      <w>phi.list</w>
-      <w>phi2poly</w>
-      <w>phi2poly.matrix</w>
-      <w>phi2tetra</w>
-      <w>phiX174Phage</w>
-      <w>phicoef</w>
-      <w>phones</w>
-      <w>phosphor</w>
-      <w>phred2ASCIIOffset</w>
-      <w>phydataplot</w>
-      <w>phylogram.plot</w>
-      <w>phymltest</w>
-      <w>phyper</w>
-      <w>physical</w>
-      <w>physical.default</w>
-      <w>pi</w>
-      <w>pi0.est</w>
-      <w>pi0est</w>
-      <w>pic</w>
-      <w>pic.ortho</w>
-      <w>pickBIC</w>
-      <w>pickSizeBest</w>
-      <w>pickSizeTolerance</w>
-      <w>pickVars</w>
-      <w>picker</w>
-      <w>pico</w>
-      <w>picoseconds</w>
-      <w>pictex</w>
-      <w>picture</w>
-      <w>pictureGrob</w>
-      <w>picturePaths</w>
-      <w>pid</w>
-      <w>pie</w>
-      <w>pie.labels</w>
-      <w>pie3D</w>
-      <w>pie3D.labels</w>
-      <w>pieGlyph</w>
-      <w>piecewise.layout</w>
-      <w>piecewiselin</w>
-      <w>pigs</w>
-      <w>pileLettersAt</w>
-      <w>pileup</w>
-      <w>pileupAsGRanges</w>
-      <w>pileupGRangesAsVariantTable</w>
-      <w>pillar</w>
-      <w>pillar_shaft</w>
-      <w>pilot</w>
-      <w>pima</w>
-      <w>pintersect</w>
-      <w>pinvgauss</w>
-      <w>pipe</w>
-      <w>pipelineIlluminaMethylation.batch</w>
-      <w>piridge</w>
-      <w>piridge.zeroes</w>
-      <w>pivots</w>
-      <w>pkgDepTools</w>
-      <w>pkgDepends</w>
-      <w>pkgStartupMessage</w>
-      <w>pkgVignettes</w>
-      <w>pkg_attach</w>
-      <w>pkg_attach2</w>
-      <w>pkg_desc</w>
-      <w>pkg_env</w>
-      <w>pkg_has_src</w>
-      <w>pkg_links_to_rcpp</w>
-      <w>pkg_load</w>
-      <w>pkg_load2</w>
-      <w>pkg_name</w>
-      <w>pkg_ns</w>
-      <w>pkg_path</w>
-      <w>pkg_version</w>
-      <w>pkgbuild</w>
-      <w>pkgbuild_process</w>
-      <w>pkgconfig</w>
-      <w>pkgload</w>
-      <w>pkgmaker</w>
-      <w>pkgreg_fetch</w>
-      <w>pkgreg_remove</w>
-      <w>pkgtest</w>
-      <w>pl.ds</w>
-      <w>place.knots</w>
-      <w>placeGrob</w>
-      <w>placeLabels</w>
-      <w>place_labels</w>
-      <w>plan</w>
-      <w>planarCanonicalOrdering</w>
-      <w>planarFaceTraversal</w>
-      <w>plant</w>
-      <w>plantTraits</w>
-      <w>plasma</w>
-      <w>plasma_retinol_MvsF</w>
-      <w>platformSigs</w>
-      <w>platform_info</w>
-      <w>playerout.costfunction</w>
-      <w>plclust</w>
-      <w>plinrain</w>
-      <w>plnorm</w>
-      <w>plogis</w>
-      <w>plogr</w>
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-      <w>plot.DMFA</w>
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-      <w>plot.FAMD</w>
-      <w>plot.GPA</w>
-      <w>plot.HCPC</w>
-      <w>plot.HMFA</w>
-      <w>plot.Krig</w>
-      <w>plot.MCA</w>
-      <w>plot.MFA</w>
-      <w>plot.Mclust</w>
-      <w>plot.MclustBootstrap</w>
-      <w>plot.MclustDA</w>
-      <w>plot.MclustDR</w>
-      <w>plot.PBmodcomp</w>
-      <w>plot.PCA</w>
-      <w>plot.ProbeSet</w>
-      <w>plot.blcTree</w>
-      <w>plot.catdes</w>
-      <w>plot.clboot</w>
-      <w>plot.clustCombi</w>
-      <w>plot.ctlcurves</w>
-      <w>plot.dbscan</w>
-      <w>plot.default</w>
-      <w>plot.dendrite</w>
-      <w>plot.densityMclust</w>
-      <w>plot.design</w>
-      <w>plot.dmap</w>
-      <w>plot.ecdf</w>
-      <w>plot.eval</w>
-      <w>plot.evonet</w>
-      <w>plot.function</w>
-      <w>plot.functional</w>
-      <w>plot.gafs</w>
-      <w>plot.gam</w>
-      <w>plot.glcTree</w>
-      <w>plot.gmmhd</w>
-      <w>plot.grenander</w>
-      <w>plot.igraph</w>
-      <w>plot.irt</w>
-      <w>plot.lars</w>
-      <w>plot.limdil</w>
-      <w>plot.lme</w>
-      <w>plot.marrayNorm</w>
-      <w>plot.marrayRaw</w>
-      <w>plot.mclustBIC</w>
-      <w>plot.mclustBootstrapLRT</w>
-      <w>plot.mclustICL</w>
-      <w>plot.mfpc</w>
-      <w>plot.mixEM</w>
-      <w>plot.mixMCMC</w>
-      <w>plot.monoreg</w>
-      <w>plot.mselm</w>
-      <w>plot.multiPhylo</w>
-      <w>plot.mvnpEM</w>
-      <w>plot.new</w>
-      <w>plot.npEM</w>
-      <w>plot.panda</w>
-      <w>plot.phylo</w>
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-      <w>plot.psych</w>
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-      <w>plot.residuals</w>
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-      <w>plot.rfpc</w>
-      <w>plot.rq.process</w>
-      <w>plot.rqs</w>
-      <w>plot.rqss</w>
-      <w>plot.safs</w>
-      <w>plot.segmented</w>
-      <w>plot.selm</w>
-      <w>plot.sim</w>
-      <w>plot.snowTimingData</w>
-      <w>plot.spEM</w>
-      <w>plot.spEMN01</w>
-      <w>plot.spam</w>
-      <w>plot.spatialDesign</w>
-      <w>plot.spatialProcess</w>
-      <w>plot.spec.coherency</w>
-      <w>plot.spec.phase</w>
-      <w>plot.sreg</w>
-      <w>plot.stepfun</w>
-      <w>plot.summary.crqs</w>
-      <w>plot.summary.rqs</w>
-      <w>plot.summary.rqss</w>
-      <w>plot.surface</w>
-      <w>plot.table.rq</w>
-      <w>plot.tclust</w>
-      <w>plot.tkm</w>
-      <w>plot.tkmeans</w>
-      <w>plot.train</w>
-      <w>plot.trls</w>
-      <w>plot.ts</w>
-      <w>plot.valstat</w>
-      <w>plot.venn</w>
-      <w>plot.vgram</w>
-      <w>plot.vgram.matrix</w>
-      <w>plot.window</w>
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-      <w>plot.zoo</w>
-      <w>plot2D.SymmModulated</w>
-      <w>plotAffyRNAdeg</w>
-      <w>plotAnnoBar</w>
-      <w>plotAnnoPie</w>
-      <w>plotAnnoPie.csAnno</w>
-      <w>plotArguments</w>
-      <w>plotAvgProf</w>
-      <w>plotAvgProf2</w>
-      <w>plotBCV</w>
-      <w>plotBeadIntensities</w>
-      <w>plotBeadLocations</w>
-      <w>plotBetasByType</w>
-      <w>plotBreakLongEdges</w>
-      <w>plotCDF</w>
-      <w>plotCI</w>
-      <w>plotCNEDistribution</w>
-      <w>plotCNEWidth</w>
-      <w>plotCVLars</w>
-      <w>plotCellData</w>
-      <w>plotChangepoint</w>
-      <w>plotChipLayout</w>
-      <w>plotChr</w>
-      <w>plotClassProbs</w>
-      <w>plotColData</w>
-      <w>plotColorBias1D</w>
-      <w>plotColorBias2D</w>
-      <w>plotColorLegend</w>
-      <w>plotCommunityDetection</w>
-      <w>plotCompetingRiskModel</w>
-      <w>plotConf</w>
-      <w>plotControlData</w>
-      <w>plotCorrPrecision</w>
-      <w>plotCorrelation</w>
-      <w>plotCounts</w>
-      <w>plotCpg</w>
-      <w>plotDS</w>
-      <w>plotDataHeatmap</w>
-      <w>plotDataScatter</w>
-      <w>plotDensities</w>
-      <w>plotDensities.EList</w>
-      <w>plotDensities.EListRaw</w>
-      <w>plotDensities.MAList</w>
-      <w>plotDensities.RGList</w>
-      <w>plotDensities.default</w>
-      <w>plotDensity</w>
-      <w>plotDensity.AffyBatch</w>
-      <w>plotDensityMclust1</w>
-      <w>plotDensityMclust2</w>
-      <w>plotDensityMclustd</w>
-      <w>plotDiffusionMap</w>
-      <w>plotDispEsts</w>
-      <w>plotDistToTSS</w>
-      <w>plotEll</w>
-      <w>plotEnrichment</w>
-      <w>plotEnrichmentBars</w>
-      <w>plotEnrichmentHeatmap</w>
-      <w>plotEvalues.MclustDR</w>
-      <w>plotExonUsage</w>
-      <w>plotExons</w>
-      <w>plotExplanatoryVariables</w>
-      <w>plotExpression</w>
-      <w>plotExpressionDefault</w>
-      <w>plotExpressionGraph</w>
-      <w>plotExpressionProfiles</w>
-      <w>plotExprsFreqVsMean</w>
-      <w>plotExprsVsTxLength</w>
-      <w>plotFB</w>
-      <w>plotFB.EListRaw</w>
-      <w>plotFB.RGList</w>
-      <w>plotFB.default</w>
-      <w>plotFDR</w>
-      <w>plotFactorBeeswarm</w>
-      <w>plotFactorCor</w>
-      <w>plotFactorHist</w>
-      <w>plotFactorScatter</w>
-      <w>plotFactorScatters</w>
-      <w>plotFeatureData</w>
-      <w>plotGOTermGraph</w>
-      <w>plotGPApartial</w>
-      <w>plotGRanges</w>
-      <w>plotGammaFit</w>
-      <w>plotGraph</w>
-      <w>plotGrowthCurves</w>
-      <w>plotGseaTable</w>
-      <w>plotH</w>
-      <w>plotHDPChangepoint</w>
-      <w>plotHierarchy</w>
-      <w>plotHighestExprs</w>
-      <w>plotHousekeepingGene</w>
-      <w>plotIllnessDeathModel</w>
-      <w>plotImage.blcTree</w>
-      <w>plotImage.glcTree</w>
-      <w>plotInterquantileWidth</w>
-      <w>plotLocation</w>
-      <w>plotLowess</w>
-      <w>plotMA</w>
-      <w>plotMA.EList</w>
-      <w>plotMA.EListRaw</w>
-      <w>plotMA.MAList</w>
-      <w>plotMA.MArrayLM</w>
-      <w>plotMA.RGList</w>
-      <w>plotMA.default</w>
-      <w>plotMA3by2</w>
-      <w>plotMAXY</w>
-      <w>plotMAhex</w>
-      <w>plotMD</w>
-      <w>plotMD.DGEExact</w>
-      <w>plotMD.DGEGLM</w>
-      <w>plotMD.DGELRT</w>
-      <w>plotMD.DGEList</w>
-      <w>plotMD.EList</w>
-      <w>plotMD.EListRaw</w>
-      <w>plotMD.MAList</w>
-      <w>plotMD.MArrayLM</w>
-      <w>plotMD.RGList</w>
-      <w>plotMD.default</w>
-      <w>plotMDS</w>
-      <w>plotMDS.DGEList</w>
-      <w>plotMDS.MDS</w>
-      <w>plotMDS.default</w>
-      <w>plotMFApartial</w>
-      <w>plotManyRegions</w>
-      <w>plotMeanVar</w>
-      <w>plotMetadata</w>
-      <w>plotMotifScores</w>
-      <w>plotMultSim</w>
-      <w>plotMultipleMotifs</w>
-      <w>plotNAs</w>
-      <w>plotNegOob</w>
-      <w>plotObsVsPred</w>
-      <w>plotOutput</w>
-      <w>plotPCA</w>
-      <w>plotPCASCE</w>
-      <w>plotPNG</w>
-      <w>plotPWF</w>
-      <w>plotPhenoData</w>
-      <w>plotPhyloCoor</w>
-      <w>plotPlatePosition</w>
-      <w>plotPrintTipLoess</w>
-      <w>plotPrintorder</w>
-      <w>plotQC</w>
-      <w>plotQLDisp</w>
-      <w>plotRGB</w>
-      <w>plotRLDF</w>
-      <w>plotRLE</w>
-      <w>plotReducedDim</w>
-      <w>plotReducedDimDefault</w>
-      <w>plotRegion</w>
-      <w>plotRegions</w>
-      <w>plotReverseCumulatives</w>
-      <w>plotRowData</w>
-      <w>plotSA</w>
-      <w>plotSample</w>
-      <w>plotSampleIntensities</w>
-      <w>plotSampleRelation</w>
-      <w>plotScater</w>
-      <w>plotSequence</w>
-      <w>plotSex</w>
-      <w>plotSmear</w>
-      <w>plotSparsity</w>
-      <w>plotSplice</w>
-      <w>plotSpliceDGE</w>
-      <w>plotState</w>
-      <w>plotStep</w>
-      <w>plotStringencyGene</w>
-      <w>plotTIFF</w>
-      <w>plotTSNE</w>
-      <w>plotTilesData</w>
-      <w>plotTopMotifsGroup</w>
-      <w>plotTopMotifsSequence</w>
-      <w>plotTopWeights</w>
-      <w>plotTracks</w>
-      <w>plotTree.blcTree</w>
-      <w>plotTree.glcTree</w>
-      <w>plotTreeTime</w>
-      <w>plotVST</w>
-      <w>plotVarianceExplained</w>
-      <w>plotViewport</w>
-      <w>plotVsnLogLik</w>
-      <w>plotWeights</w>
-      <w>plotWeightsHeatmap</w>
-      <w>plotWithHighlights</w>
-      <w>plotZ</w>
-      <w>plotZbyTF</w>
-      <w>plot_DiscrFact_p2</w>
-      <w>plot_DiscrFact_p3</w>
-      <w>plot_R_NX</w>
-      <w>plot_annotation</w>
-      <w>plot_bg</w>
-      <w>plot_categorical</w>
-      <w>plot_celltype_associations</w>
-      <w>plot_closest</w>
-      <w>plot_coannotations</w>
-      <w>plot_crop</w>
-      <w>plot_dendro</w>
-      <w>plot_dendrogram</w>
-      <w>plot_geo</w>
-      <w>plot_grid</w>
-      <w>plot_hex</w>
-      <w>plot_hierarchy</w>
-      <w>plot_horiz.dendrogram</w>
-      <w>plot_ly</w>
-      <w>plot_mapbox</w>
-      <w>plot_mnsl</w>
-      <w>plot_model</w>
-      <w>plot_model_pars</w>
-      <w>plot_numerical</w>
-      <w>plot_numerical_coannotations</w>
-      <w>plot_to_gtable</w>
-      <w>plotbyfactor</w>
-      <w>plotchazuh</w>
-      <w>plotcluster</w>
-      <w>plotcorr</w>
-      <w>plotcov</w>
-      <w>plotcp</w>
-      <w>plotdenuh</w>
-      <w>plotdist</w>
-      <w>plotdistcens</w>
-      <w>plotellipses</w>
-      <w>plotexpRMM</w>
-      <w>plotfeatureCoverage</w>
-      <w>plotfeaturetypeCounts</w>
-      <w>plotgradidf</w>
-      <w>plotgraduh</w>
-      <w>plothazuh</w>
-      <w>plotlines</w>
-      <w>plotly</w>
-      <w>plotlyM</w>
-      <w>plotlyOutput</w>
-      <w>plotlyParm</w>
-      <w>plotlyProxy</w>
-      <w>plotlyProxyInvoke</w>
-      <w>plotlySave</w>
-      <w>plotly_IMAGE</w>
-      <w>plotly_POST</w>
-      <w>plotly_build</w>
-      <w>plotly_data</w>
-      <w>plotly_empty</w>
-      <w>plotly_example</w>
-      <w>plotly_json</w>
-      <w>plotmathTranslate</w>
-      <w>plotmeans</w>
-      <w>plotp</w>
-      <w>plotpsummaryM</w>
-      <w>plotrix</w>
-      <w>plotseq</w>
-      <w>plotseq.npEM</w>
-      <w>plotspRMM</w>
-      <w>plotsurvidf</w>
-      <w>plotsurvuh</w>
-      <w>plotweibullRMM</w>
-      <w>plpFiles</w>
-      <w>plpFlag</w>
-      <w>plpMaxDepth</w>
-      <w>plpMinBaseQuality</w>
-      <w>plpMinDepth</w>
-      <w>plpMinMapQuality</w>
-      <w>plpParam</w>
-      <w>plpWhat</w>
-      <w>plpWhich</w>
-      <w>plpYieldAll</w>
-      <w>plpYieldBy</w>
-      <w>plpYieldSize</w>
-      <w>pls</w>
-      <w>pls.options</w>
-      <w>plsBag</w>
-      <w>plsda</w>
-      <w>plsmo</w>
-      <w>plsr</w>
-      <w>pltree</w>
-      <w>pluck</w>
-      <w>pluton</w>
-      <w>plyr</w>
-      <w>pm</w>
-      <w>pm.abstGrep</w>
-      <w>pm.getabst</w>
-      <w>pm.titles</w>
-      <w>pmAbst2HTML</w>
-      <w>pmap</w>
-      <w>pmapFromAlignments</w>
-      <w>pmapFromTranscripts</w>
-      <w>pmapToAlignments</w>
-      <w>pmapToTranscripts</w>
-      <w>pmap_chr</w>
-      <w>pmap_dbl</w>
-      <w>pmap_df</w>
-      <w>pmap_dfc</w>
-      <w>pmap_dfr</w>
-      <w>pmap_int</w>
-      <w>pmap_lgl</w>
-      <w>pmatch</w>
-      <w>pmatchPattern</w>
-      <w>pmax</w>
-      <w>pmax.int</w>
-      <w>pmax.sa</w>
-      <w>pmax2</w>
-      <w>pmcorrect.mas</w>
-      <w>pmcorrect.methods</w>
-      <w>pmcorrect.pmonly</w>
-      <w>pmcorrect.subtractmm</w>
-      <w>pmid</w>
-      <w>pmid2MIAME</w>
-      <w>pmidQuery</w>
-      <w>pmin</w>
-      <w>pmin.int</w>
-      <w>pmin.sa</w>
-      <w>pmin2</w>
-      <w>pmindex</w>
-      <w>pmnorm</w>
-      <w>pmsc</w>
-      <w>pmsn</w>
-      <w>pmst</w>
-      <w>pmt</w>
-      <w>pmvalog</w>
-      <w>pmvevd</w>
-      <w>pmvlog</w>
-      <w>pmvnorm</w>
-      <w>pmvt</w>
-      <w>pnbinom</w>
-      <w>png</w>
-      <w>pngNeedle</w>
-      <w>pnnls</w>
-      <w>pnnqp</w>
-      <w>pnorMix</w>
-      <w>pnorm</w>
-      <w>pnt.in.poly</w>
-      <w>pnweibull</w>
-      <w>poTest</w>
-      <w>point.in.polygon</w>
-      <w>pointDistance</w>
-      <w>pointLabel</w>
-      <w>pointList</w>
-      <w>points</w>
-      <w>points.default</w>
-      <w>points.functional</w>
-      <w>points.segmented</w>
-      <w>points2grid</w>
-      <w>pointsGrob</w>
-      <w>poison</w>
-      <w>poison.text</w>
-      <w>poisons</w>
-      <w>poisregmix.init</w>
-      <w>poisregmixEM</w>
-      <w>poisson</w>
-      <w>poisson.lvm</w>
-      <w>poisson.test</w>
-      <w>poissonGoodnessOfFit</w>
-      <w>poke_vars</w>
-      <w>pol2cart</w>
-      <w>polar</w>
-      <w>polar.plot</w>
-      <w>polar2rect</w>
-      <w>polarLAB</w>
-      <w>polarLUV</w>
-      <w>poll</w>
-      <w>polr</w>
-      <w>poly</w>
-      <w>poly.calc</w>
-      <w>poly.from.roots</w>
-      <w>poly.from.values</w>
-      <w>poly.from.zeros</w>
-      <w>poly.image</w>
-      <w>poly.image.regrid</w>
-      <w>poly.mat</w>
-      <w>poly.orth</w>
-      <w>polySpline</w>
-      <w>polyarea</w>
-      <w>polychoric</w>
-      <w>polydi</w>
-      <w>polydot</w>
-      <w>polygon</w>
-      <w>polygon.shadow</w>
-      <w>polygonGrob</w>
-      <w>polygon_regular</w>
-      <w>polygons</w>
-      <w>polylineGrob</w>
-      <w>polylist</w>
-      <w>polym</w>
-      <w>polyn</w>
-      <w>polyn.eval</w>
-      <w>polynFilter</w>
-      <w>polynom</w>
-      <w>polynomial</w>
-      <w>polypath</w>
-      <w>polyroot</w>
-      <w>polys.plot</w>
-      <w>polyserial</w>
-      <w>pomodm</w>
-      <w>ponAbe2.ensGene.LENGTH</w>
-      <w>ponAbe2.geneSymbol.LENGTH</w>
-      <w>ponAbe2.genscan.LENGTH</w>
-      <w>ponAbe2.nscanGene.LENGTH</w>
-      <w>ponAbe2.refGene.LENGTH</w>
-      <w>ponAbe2.xenoRefGene.LENGTH</w>
-      <w>poolVar</w>
-      <w>pooledSD</w>
-      <w>pop</w>
-      <w>pop.sim</w>
-      <w>pop.viewport</w>
-      <w>popBackupFile</w>
-      <w>popBackupFile.default</w>
-      <w>popMessage</w>
-      <w>popMessage.TextStatusBar</w>
-      <w>popState</w>
-      <w>popState.Verbose</w>
-      <w>popTemporaryFile</w>
-      <w>popTemporaryFile.default</w>
-      <w>popViewport</w>
-      <w>popower</w>
-      <w>populate</w>
-      <w>populateDB</w>
-      <w>populate_env</w>
-      <w>population</w>
-      <w>population2010</w>
-      <w>porder</w>
-      <w>port</w>
-      <w>portpirie</w>
-      <w>pos</w>
-      <w>pos.to.env</w>
-      <w>posPredValue</w>
-      <w>posamsize</w>
-      <w>poscontPlot</w>
-      <w>posdefify</w>
-      <w>position</w>
-      <w>positionFilter</w>
-      <w>position_beeswarm</w>
-      <w>position_dodge</w>
-      <w>position_dodge2</w>
-      <w>position_fill</w>
-      <w>position_identity</w>
-      <w>position_jitter</w>
-      <w>position_jitterdodge</w>
-      <w>position_nudge</w>
-      <w>position_points_jitter</w>
-      <w>position_points_sina</w>
-      <w>position_quasirandom</w>
-      <w>position_raincloud</w>
-      <w>position_stack</w>
-      <w>possibleDates</w>
-      <w>possibleExtends</w>
-      <w>possibly</w>
-      <w>possumDiv</w>
-      <w>post</w>
-      <w>post.beta</w>
-      <w>postDrawDetails</w>
-      <w>postForm</w>
-      <w>postNode</w>
-      <w>postResample</w>
-      <w>postdoc</w>
-      <w>posterior</w>
-      <w>posterior_interval</w>
-      <w>posterior_linpred</w>
-      <w>posterior_predict</w>
-      <w>postorder</w>
-      <w>postponeAction</w>
-      <w>postprocess.prop.part</w>
-      <w>postscript</w>
-      <w>postscriptFonts</w>
-      <w>potatoes</w>
-      <w>pottery</w>
-      <w>poulet</w>
-      <w>poverlaps</w>
-      <w>poweRlaw</w>
-      <w>power</w>
-      <w>power.anova.test</w>
-      <w>power.fisher.test</w>
-      <w>power.law.fit</w>
-      <w>power.prop.test</w>
-      <w>power.t.test</w>
-      <w>powerTransform</w>
-      <w>power_centrality</w>
-      <w>powerboost</w>
-      <w>powerpoint_presentation</w>
-      <w>pp</w>
-      <w>ppcomp</w>
-      <w>ppcompcens</w>
-      <w>ppgetregion</w>
-      <w>ppinit</w>
-      <w>pplcon</w>
-      <w>ppldis</w>
-      <w>pplik</w>
-      <w>ppoints</w>
-      <w>ppois</w>
-      <w>ppr</w>
-      <w>ppregion</w>
-      <w>ppset.ttest</w>
-      <w>ppsetApply</w>
-      <w>ppv</w>
-      <w>prList</w>
-      <w>prSummary</w>
-      <w>prType</w>
-      <w>pr_DB</w>
-      <w>pr_dist2simil</w>
-      <w>pr_fetch</w>
-      <w>pr_finish</w>
-      <w>pr_init</w>
-      <w>pr_pause</w>
-      <w>pr_pull</w>
-      <w>pr_pull_upstream</w>
-      <w>pr_push</w>
-      <w>pr_simil2dist</w>
-      <w>pr_sync</w>
-      <w>pr_view</w>
-      <w>prab.sarestimate</w>
-      <w>prabclus</w>
-      <w>prabclust</w>
-      <w>prabinit</w>
-      <w>prabtest</w>
-      <w>prcomp</w>
-      <w>prcomp_irlba</w>
-      <w>pre</w>
-      <w>preDrawDetails</w>
-      <w>preProcess</w>
-      <w>precede</w>
-      <w>precip</w>
-      <w>precision</w>
-      <w>precmat</w>
-      <w>precmat.GMRFreglat</w>
-      <w>precmat.IGMRFirreglat</w>
-      <w>precmat.IGMRFreglat</w>
-      <w>precmat.RW1</w>
-      <w>precmat.RW2</w>
-      <w>precmat.RWn</w>
-      <w>precmat.season</w>
-      <w>predFC</w>
-      <w>predFC.DGEList</w>
-      <w>predFC.default</w>
-      <w>predFCm</w>
-      <w>predORF</w>
-      <w>predgain</w>
-      <w>predict</w>
-      <w>predict.CA</w>
-      <w>predict.FAMD</w>
-      <w>predict.Krig</w>
-      <w>predict.LogitBoost</w>
-      <w>predict.MCA</w>
-      <w>predict.Mclust</w>
-      <w>predict.MclustDA</w>
-      <w>predict.MclustDR</w>
-      <w>predict.PCA</w>
-      <w>predict.Tps</w>
-      <w>predict.bagEarth</w>
-      <w>predict.bam</w>
-      <w>predict.blcTree</w>
-      <w>predict.crq</w>
-      <w>predict.crqs</w>
-      <w>predict.dbscan</w>
-      <w>predict.densityMclust</w>
-      <w>predict.ellipsoid</w>
-      <w>predict.fastTps</w>
-      <w>predict.gafs</w>
-      <w>predict.gam</w>
-      <w>predict.glcTree</w>
-      <w>predict.glm</w>
-      <w>predict.interp.surface</w>
-      <w>predict.ipredknn</w>
-      <w>predict.lars</w>
-      <w>predict.lm</w>
-      <w>predict.mKrig</w>
-      <w>predict.nlrq</w>
-      <w>predict.psych</w>
-      <w>predict.qsreg</w>
-      <w>predict.qss1</w>
-      <w>predict.qss2</w>
-      <w>predict.rq</w>
-      <w>predict.rq.process</w>
-      <w>predict.rqs</w>
-      <w>predict.rqss</w>
-      <w>predict.segmented</w>
-      <w>predict.selm</w>
-      <w>predict.sreg</w>
-      <w>predict.surface</w>
-      <w>predict.surface.default</w>
-      <w>predict.train</w>
-      <w>predict.trls</w>
-      <w>predict2D.MclustDR</w>
-      <w>predictCoding</w>
-      <w>predictDerivative.Krig</w>
-      <w>predictSE</w>
-      <w>predictSE.Krig</w>
-      <w>predictSE.mKrig</w>
-      <w>predictSEUsingKrigA</w>
-      <w>predictSurface</w>
-      <w>predictSurface.Krig</w>
-      <w>predictSurface.default</w>
-      <w>predictSurface.fastTps</w>
-      <w>predictSurface.mKrig</w>
-      <w>predictSurfaceSE</w>
-      <w>predictSurfaceSE.default</w>
-      <w>predictSurvIndividual</w>
-      <w>predict_edges</w>
-      <w>prediction</w>
-      <w>prediction.strength</w>
-      <w>predictionFunction</w>
-      <w>predictions</w>
-      <w>predictive_error</w>
-      <w>predictive_interval</w>
-      <w>predictlvm</w>
-      <w>predictors</w>
-      <w>prednames</w>
-      <w>predplot</w>
-      <w>pref</w>
-      <w>preference.game</w>
-      <w>prefit</w>
-      <w>prefix_match</w>
-      <w>prefpls</w>
-      <w>prep</w>
-      <w>prepMultiAssay</w>
-      <w>prepanel.Dotplot</w>
-      <w>prepanel.Ecdf</w>
-      <w>prepanel.default.bwplot</w>
-      <w>prepanel.default.cloud</w>
-      <w>prepanel.default.densityplot</w>
-      <w>prepanel.default.histogram</w>
-      <w>prepanel.default.levelplot</w>
-      <w>prepanel.default.parallel</w>
-      <w>prepanel.default.qq</w>
-      <w>prepanel.default.qqmath</w>
-      <w>prepanel.default.splom</w>
-      <w>prepanel.default.xyplot</w>
-      <w>prepanel.ecdfplot</w>
-      <w>prepanel.horizonplot</w>
-      <w>prepanel.lmline</w>
-      <w>prepanel.loess</w>
-      <w>prepanel.mapplot</w>
-      <w>prepanel.qqmathline</w>
-      <w>prepanel.rootogram</w>
-      <w>prepanel.segplot</w>
-      <w>prepanel.spline</w>
-      <w>prepanel.tmd.default</w>
-      <w>prepanel.tmd.qqmath</w>
-      <w>prepanel.xYplot</w>
-      <w>prepare</w>
-      <w>prepare.ggdend</w>
-      <w>prepare.quantile.groups</w>
-      <w>prepareMOFA</w>
-      <w>prepend</w>
-      <w>prependContent</w>
-      <w>prependTab</w>
-      <w>preplot</w>
-      <w>prepper</w>
-      <w>preproc</w>
-      <w>preprocessCore</w>
-      <w>preprocessFunnorm</w>
-      <w>preprocessIllumina</w>
-      <w>preprocessIlluminaMethylation</w>
-      <w>preprocessMethod</w>
-      <w>preprocessNoob</w>
-      <w>preprocessQuantile</w>
-      <w>preprocessRaw</w>
-      <w>preprocessReads</w>
-      <w>preprocessSWAN</w>
-      <w>presidential</w>
-      <w>presidents</w>
-      <w>pressure</w>
-      <w>prettify</w>
-      <w>pretty</w>
-      <w>pretty.default</w>
-      <w>pretty10exp</w>
-      <w>prettyNum</w>
-      <w>pretty_breaks</w>
-      <w>pretty_bytes</w>
-      <w>pretty_dates</w>
-      <w>pretty_dt</w>
-      <w>pretty_ms</w>
-      <w>pretty_sec</w>
-      <w>prettydoc</w>
-      <w>prettyunits</w>
-      <w>previewRd</w>
-      <w>previewSql</w>
-      <w>priPac1.xenoRefGene.LENGTH</w>
-      <w>prim.minST</w>
-      <w>primal</w>
-      <w>primary_selection</w>
-      <w>primes</w>
-      <w>principal</w>
-      <w>princomp</w>
-      <w>print</w>
-      <w>print.AAbin</w>
-      <w>print.AovSum</w>
-      <w>print.AsIs</w>
-      <w>print.BasicObject</w>
-      <w>print.BootRefFreeEwasModel</w>
-      <w>print.CA</w>
-      <w>print.CaGalt</w>
-      <w>print.CapturedEvaluation</w>
-      <w>print.Class</w>
-      <w>print.CmdArgsFunction</w>
-      <w>print.DLLInfo</w>
-      <w>print.DLLInfoList</w>
-      <w>print.DLLRegisteredRoutines</w>
-      <w>print.DMS</w>
-      <w>print.DNAbin</w>
-      <w>print.Date</w>
-      <w>print.DiscrFact</w>
-      <w>print.Dlist</w>
-      <w>print.Exception</w>
-      <w>print.FAMD</w>
-      <w>print.GPA</w>
-      <w>print.GString</w>
-      <w>print.GenericSummary</w>
-      <w>print.HCPC</w>
-      <w>print.HMFA</w>
-      <w>print.Interface</w>
-      <w>print.KRmodcomp</w>
-      <w>print.Krig</w>
-      <w>print.MCA</w>
-      <w>print.MFA</w>
-      <w>print.Mclust</w>
-      <w>print.MclustBootstrap</w>
-      <w>print.MclustDA</w>
-      <w>print.MclustDR</w>
-      <w>print.MclustDRsubsel</w>
-      <w>print.NativeRoutineList</w>
-      <w>print.NullVerbose</w>
-      <w>print.Object</w>
-      <w>print.PBmodcomp</w>
-      <w>print.PCA</w>
-      <w>print.POSIXct</w>
-      <w>print.POSIXlt</w>
-      <w>print.RefFreeCellMix</w>
-      <w>print.RefFreeEwasModel</w>
-      <w>print.Verbose</w>
-      <w>print.alleleobject</w>
-      <w>print.anova.gam</w>
-      <w>print.anova.rq</w>
-      <w>print.bit</w>
-      <w>print.bitwhich</w>
-      <w>print.blcTree</w>
-      <w>print.by</w>
-      <w>print.catdes</w>
-      <w>print.char.matrix</w>
-      <w>print.clboot</w>
-      <w>print.clustCombi</w>
-      <w>print.clusterbenchstats</w>
-      <w>print.comprabclust</w>
-      <w>print.condition</w>
-      <w>print.connection</w>
-      <w>print.crq</w>
-      <w>print.ctlcurves</w>
-      <w>print.data.frame</w>
-      <w>print.dbscan</w>
-      <w>print.default</w>
-      <w>print.difftime</w>
-      <w>print.dmap</w>
-      <w>print.dynrq</w>
-      <w>print.dynrqs</w>
-      <w>print.eigen</w>
-      <w>print.factor</w>
-      <w>print.function</w>
-      <w>print.gam</w>
-      <w>print.glcTree</w>
-      <w>print.gmmhd</w>
-      <w>print.hc</w>
-      <w>print.hexmode</w>
-      <w>print.igraph</w>
-      <w>print.lars</w>
-      <w>print.libraryIQR</w>
-      <w>print.limdil</w>
-      <w>print.listof</w>
-      <w>print.mKrig</w>
-      <w>print.mKrigSummary</w>
-      <w>print.mclustBIC</w>
-      <w>print.mclustBootstrapLRT</w>
-      <w>print.mclustICL</w>
-      <w>print.mclustLoglik</w>
-      <w>print.mfpc</w>
-      <w>print.mvnpEM</w>
-      <w>print.nlrq</w>
-      <w>print.nnclean</w>
-      <w>print.noquote</w>
-      <w>print.npEM</w>
-      <w>print.numeric_version</w>
-      <w>print.octmode</w>
-      <w>print.packageInfo</w>
-      <w>print.permTestResults</w>
-      <w>print.phylo</w>
-      <w>print.physical</w>
-      <w>print.prab</w>
-      <w>print.prabclust</w>
-      <w>print.predstr</w>
-      <w>print.proc_time</w>
-      <w>print.psych</w>
-      <w>print.qsreg</w>
-      <w>print.restart</w>
-      <w>print.rfpc</w>
-      <w>print.ri</w>
-      <w>print.rle</w>
-      <w>print.rq</w>
-      <w>print.rqs</w>
-      <w>print.rqss</w>
-      <w>print.segmented</w>
-      <w>print.shapehead</w>
-      <w>print.simple.list</w>
-      <w>print.slm</w>
-      <w>print.snowTimingData</w>
-      <w>print.spam</w>
-      <w>print.spam.chol.NgPeyton</w>
-      <w>print.spatialDesign</w>
-      <w>print.spatialProcess</w>
-      <w>print.spatialProcessSummary</w>
-      <w>print.srcfile</w>
-      <w>print.srcref</w>
-      <w>print.sreg</w>
-      <w>print.summary.Krig</w>
-      <w>print.summary.Mclust</w>
-      <w>print.summary.MclustBootstrap</w>
-      <w>print.summary.MclustDA</w>
-      <w>print.summary.MclustDR</w>
-      <w>print.summary.clustCombi</w>
-      <w>print.summary.cquality</w>
-      <w>print.summary.crq</w>
-      <w>print.summary.crqs</w>
-      <w>print.summary.dynrq</w>
-      <w>print.summary.dynrqs</w>
-      <w>print.summary.gam</w>
-      <w>print.summary.gmmhd</w>
-      <w>print.summary.mclustICL</w>
-      <w>print.summary.mergenorm</w>
-      <w>print.summary.mfpc</w>
-      <w>print.summary.mvnpEM</w>
-      <w>print.summary.nlrq</w>
-      <w>print.summary.npEM</w>
-      <w>print.summary.prabtest</w>
-      <w>print.summary.rfpc</w>
-      <w>print.summary.rq</w>
-      <w>print.summary.rqs</w>
-      <w>print.summary.rqss</w>
-      <w>print.summary.segmented</w>
-      <w>print.summary.slm</w>
-      <w>print.summary.sreg</w>
-      <w>print.summary.table</w>
-      <w>print.summaryBootRefFreeEwasModel</w>
-      <w>print.summaryDefault</w>
-      <w>print.summaryPB</w>
-      <w>print.summarySpatialDesign</w>
-      <w>print.table</w>
-      <w>print.tclust</w>
-      <w>print.tkm</w>
-      <w>print.train</w>
-      <w>print.valstat</w>
-      <w>print.varwisetables</w>
-      <w>print.virtual</w>
-      <w>print.warnings</w>
-      <w>print.xtable</w>
-      <w>print.xtableFtable</w>
-      <w>print.xtableList</w>
-      <w>print.xtableMatharray</w>
-      <w>printAtomicVectorInAGrid</w>
-      <w>printCoefmat</w>
-      <w>printError</w>
-      <w>printFlush</w>
-      <w>printGCVWarnings</w>
-      <w>printGenes</w>
-      <w>printGraph</w>
-      <w>printHTML.trackInfo</w>
-      <w>printHTMLProtocol</w>
-      <w>printHead</w>
-      <w>printHypothesis</w>
-      <w>printJUnitProtocol</w>
-      <w>printSpMatrix</w>
-      <w>printSpMatrix2</w>
-      <w>printStackTrace</w>
-      <w>printStackTrace.Exception</w>
-      <w>printStrToChar</w>
-      <w>printTable2</w>
-      <w>printTextProtocol</w>
-      <w>printToChar</w>
-      <w>print_all</w>
-      <w>print_dims</w>
-      <w>print_help</w>
-      <w>print_if_interactive</w>
-      <w>print_labels</w>
-      <w>print_tagged_na</w>
-      <w>printcp</w>
-      <w>printer</w>
-      <w>printer_callback</w>
-      <w>printf</w>
-      <w>printf.NullVerbose</w>
-      <w>printf.Verbose</w>
-      <w>printf.default</w>
-      <w>printorder</w>
-      <w>printtipWeights</w>
-      <w>prior</w>
-      <w>priorControl</w>
-      <w>priorInfo</w>
-      <w>prior_summary</w>
-      <w>prmat</w>
-      <w>prmatrix</w>
-      <w>prn</w>
-      <w>prob.model</w>
-      <w>probFunction</w>
-      <w>probabilityAxis</w>
-      <w>probabilityToSnpMatrix</w>
-      <w>probability_trans</w>
-      <w>probe.450K.VCs.af</w>
-      <w>probe.features</w>
-      <w>probe.features.epic</w>
-      <w>probe450kfemanno</w>
-      <w>probeEPICfemanno</w>
-      <w>probeID2nuID</w>
-      <w>probeInfoALL.epic.lv</w>
-      <w>probeInfoALL.lv</w>
-      <w>probeNAs</w>
-      <w>probeNames</w>
-      <w>probeRangeMapper</w>
-      <w>probeSetSummary</w>
-      <w>probes</w>
-      <w>probes2MAP</w>
-      <w>probes2Path</w>
-      <w>probesByLL</w>
-      <w>probesToChrom</w>
-      <w>probeset</w>
-      <w>probit.lvm</w>
-      <w>probit_trans</w>
-      <w>problems</w>
-      <w>probplot</w>
-      <w>proc.time</w>
-      <w>process</w>
-      <w>process.events</w>
-      <w>processAmplicons</w>
-      <w>processSwathData</w>
-      <w>processXInclude</w>
-      <w>processingInstruction.SAX</w>
-      <w>processx</w>
-      <w>processx_conn_close</w>
-      <w>processx_conn_is_incomplete</w>
-      <w>processx_conn_read_chars</w>
-      <w>processx_conn_read_lines</w>
-      <w>processx_conn_write</w>
-      <w>procformula</w>
-      <w>procrustes</w>
-      <w>prod</w>
-      <w>prod.na</w>
-      <w>prodlim</w>
-      <w>produceGEOPlatformFile</w>
-      <w>produceGEOSampleInfoTemplate</w>
-      <w>produceGEOSubmissionFile</w>
-      <w>produceMethylationGEOSubmissionFile</w>
-      <w>product</w>
-      <w>prof</w>
-      <w>profile</w>
-      <w>profile.selm</w>
-      <w>profile2d</w>
-      <w>profileSites</w>
-      <w>progress</w>
-      <w>progressBar</w>
-      <w>progress_bar</w>
-      <w>progress_estimated</w>
-      <w>progress_none</w>
-      <w>progress_text</w>
-      <w>progress_time</w>
-      <w>progress_tk</w>
-      <w>progress_win</w>
-      <w>prohibitGeneric</w>
-      <w>proj</w>
-      <w>proj4string</w>
-      <w>proj_activate</w>
-      <w>proj_get</w>
-      <w>proj_path</w>
-      <w>proj_set</w>
-      <w>proj_sitrep</w>
-      <w>projectExtent</w>
-      <w>projectMix</w>
-      <w>projectRaster</w>
-      <w>projection</w>
-      <w>projectionplotvariables</w>
-      <w>projpar.MclustDR</w>
-      <w>promax</w>
-      <w>promise</w>
-      <w>promise_all</w>
-      <w>promise_map</w>
-      <w>promise_race</w>
-      <w>promise_reduce</w>
-      <w>promise_reject</w>
-      <w>promise_resolve</w>
-      <w>promises</w>
-      <w>promoter</w>
-      <w>promotergene</w>
-      <w>promoters</w>
-      <w>prompt</w>
-      <w>promptAndSave</w>
-      <w>promptAndSave.Settings</w>
-      <w>promptClass</w>
-      <w>promptData</w>
-      <w>promptImport</w>
-      <w>promptMethods</w>
-      <w>promptPackage</w>
-      <w>promptPackageSexpr</w>
-      <w>promptUsage</w>
-      <w>prop.clades</w>
-      <w>prop.correct</w>
-      <w>prop.part</w>
-      <w>prop.table</w>
-      <w>prop.test</w>
-      <w>prop.trend.test</w>
-      <w>propTrueNull</w>
-      <w>propbrk</w>
-      <w>propexpr</w>
-      <w>prose_index</w>
-      <w>protan</w>
-      <w>protanomaly_cvd</w>
-      <w>protectMetachar</w>
-      <w>protect_math</w>
-      <w>proteins</w>
-      <w>protocolData</w>
-      <w>prototype</w>
-      <w>provideDimnames</w>
-      <w>provider</w>
-      <w>providerVersion</w>
-      <w>proxy</w>
-      <w>prselect</w>
-      <w>prt.DEBUG</w>
-      <w>prune</w>
-      <w>prune.rpart</w>
-      <w>pruneMap</w>
-      <w>prune_common_subtrees.dendlist</w>
-      <w>prune_leaf</w>
-      <w>prweibull</w>
-      <w>ps</w>
-      <w>ps.do</w>
-      <w>ps.end</w>
-      <w>ps.latex</w>
-      <w>ps.options</w>
-      <w>ps_boot_time</w>
-      <w>ps_children</w>
-      <w>ps_cmdline</w>
-      <w>ps_connections</w>
-      <w>ps_cpu_count</w>
-      <w>ps_cpu_times</w>
-      <w>ps_create_time</w>
-      <w>ps_cwd</w>
-      <w>ps_environ</w>
-      <w>ps_environ_raw</w>
-      <w>ps_exe</w>
-      <w>ps_find_tree</w>
-      <w>ps_gids</w>
-      <w>ps_handle</w>
-      <w>ps_interrupt</w>
-      <w>ps_is_running</w>
-      <w>ps_is_supported</w>
-      <w>ps_kill</w>
-      <w>ps_kill_tree</w>
-      <w>ps_mark_tree</w>
-      <w>ps_memory_info</w>
-      <w>ps_name</w>
-      <w>ps_num_fds</w>
-      <w>ps_num_threads</w>
-      <w>ps_open_files</w>
-      <w>ps_os_type</w>
-      <w>ps_parent</w>
-      <w>ps_pid</w>
-      <w>ps_pids</w>
-      <w>ps_ppid</w>
-      <w>ps_resume</w>
-      <w>ps_send_signal</w>
-      <w>ps_status</w>
-      <w>ps_suspend</w>
-      <w>ps_terminal</w>
-      <w>ps_terminate</w>
-      <w>ps_uids</w>
-      <w>ps_username</w>
-      <w>ps_users</w>
-      <w>psc</w>
-      <w>pscore.test</w>
-      <w>psegments3d</w>
-      <w>psetdiff</w>
-      <w>pseudo_log_trans</w>
-      <w>pseudobma_weights</w>
-      <w>psi.bisquare</w>
-      <w>psi.hampel</w>
-      <w>psi.huber</w>
-      <w>psiFunc</w>
-      <w>psigamma</w>
-      <w>psignrank</w>
-      <w>psis</w>
-      <w>psis_n_eff_values</w>
-      <w>psislw</w>
-      <w>pskill</w>
-      <w>psms</w>
-      <w>psn</w>
-      <w>psnice</w>
-      <w>pspline</w>
-      <w>pst</w>
-      <w>pstamp</w>
-      <w>psubAxt</w>
-      <w>psummary</w>
-      <w>psurvreg</w>
-      <w>psva</w>
-      <w>psych</w>
-      <w>psych.misc</w>
-      <w>psychademic</w>
-      <w>pt</w>
-      <w>ptail</w>
-      <w>ptext3d</w>
-      <w>ptukey</w>
-      <w>pubDate</w>
-      <w>pubMedAbst</w>
-      <w>pubMedIds</w>
-      <w>pubmed</w>
-      <w>pull</w>
-      <w>pulpfiber</w>
-      <w>punch_card</w>
-      <w>punif</w>
-      <w>punion</w>
-      <w>puny_decode</w>
-      <w>puny_encode</w>
-      <w>purl</w>
-      <w>purrr</w>
-      <w>push</w>
-      <w>push.relabel.max.flow</w>
-      <w>push.viewport</w>
-      <w>pushBack</w>
-      <w>pushBackLength</w>
-      <w>pushBackupFile</w>
-      <w>pushBackupFile.default</w>
-      <w>pushHexport</w>
-      <w>pushState</w>
-      <w>pushState.Verbose</w>
-      <w>pushTemporaryFile</w>
-      <w>pushTemporaryFile.default</w>
-      <w>pushViewport</w>
-      <w>pushpin</w>
-      <w>put.data</w>
-      <w>putHcap</w>
-      <w>putHfig</w>
-      <w>putKey</w>
-      <w>putKeyEmpty</w>
-      <w>putPlot</w>
-      <w>pval.detect</w>
-      <w>pval.estimate.eta0</w>
-      <w>pvalmat</w>
-      <w>pvals</w>
-      <w>pvalue</w>
-      <w>pvalueCutoff</w>
-      <w>pvalueFormatter</w>
-      <w>pvalue_format</w>
-      <w>pvalues</w>
-      <w>pvclust_edges</w>
-      <w>pvclust_show_signif</w>
-      <w>pvclust_show_signif_gradient</w>
-      <w>pvec</w>
-      <w>pvrect2</w>
-      <w>pw561</w>
-      <w>pwalk</w>
-      <w>pweibull</w>
-      <w>pwilcox</w>
-      <w>pwod</w>
-      <w>pyears</w>
-      <w>pyramid.plot</w>
-      <w>q</w>
-      <w>q2qnbinom</w>
-      <w>q2qpois</w>
-      <w>qDiptab</w>
-      <w>qFNCHypergeo</w>
-      <w>qWNCHypergeo</w>
-      <w>qa</w>
-      <w>qa2</w>
-      <w>qbeta</w>
-      <w>qbinom</w>
-      <w>qbirthday</w>
-      <w>qc.probe.plot</w>
-      <w>qcData</w>
-      <w>qcReport</w>
-      <w>qcauchy</w>
-      <w>qcbvnonpar</w>
-      <w>qchisq</w>
-      <w>qcor0</w>
-      <w>qcplot</w>
-      <w>qda</w>
-      <w>qday</w>
-      <w>qdensity</w>
-      <w>qdiscrete</w>
-      <w>qerror</w>
-      <w>qexp</w>
-      <w>qextreme</w>
-      <w>qf</w>
-      <w>qfrechet</w>
-      <w>qgamma</w>
-      <w>qgeom</w>
-      <w>qgev</w>
-      <w>qgpd</w>
-      <w>qgumbel</w>
-      <w>qhalfnorm</w>
-      <w>qhyper</w>
-      <w>qinvgauss</w>
-      <w>qkulczynski</w>
-      <w>qlibrary</w>
-      <w>qlnorm</w>
-      <w>qlogis</w>
-      <w>qmedist</w>
-      <w>qmvnorm</w>
-      <w>qmvt</w>
-      <w>qn</w>
-      <w>qnamePrefixEnd</w>
-      <w>qnameSuffixStart</w>
-      <w>qnarrow</w>
-      <w>qnbinom</w>
-      <w>qnorMix</w>
-      <w>qnorm</w>
-      <w>qnweibull</w>
-      <w>qp</w>
-      <w>qplot</w>
-      <w>qpois</w>
-      <w>qq</w>
-      <w>qq.gam</w>
-      <w>qq.plot</w>
-      <w>qqPlot</w>
-      <w>qqcomp</w>
-      <w>qqcompcens</w>
-      <w>qqf</w>
-      <w>qqline</w>
-      <w>qqmath</w>
-      <w>qqnorm</w>
-      <w>qqnorm.aov</w>
-      <w>qqp</w>
-      <w>qqplot</w>
-      <w>qqt</w>
-      <w>qr</w>
-      <w>qr.Q</w>
-      <w>qr.R</w>
-      <w>qr.X</w>
-      <w>qr.coef</w>
-      <w>qr.default</w>
-      <w>qr.fitted</w>
-      <w>qr.q2ty</w>
-      <w>qr.qty</w>
-      <w>qr.qy</w>
-      <w>qr.resid</w>
-      <w>qr.solve</w>
-      <w>qr.yq2</w>
-      <w>qrR</w>
-      <w>qrequire</w>
-      <w>qres.binom</w>
-      <w>qres.default</w>
-      <w>qres.gamma</w>
-      <w>qres.invgauss</w>
-      <w>qres.nbinom</w>
-      <w>qres.pois</w>
-      <w>qres.tweedie</w>
-      <w>qresid</w>
-      <w>qresiduals</w>
-      <w>qrisk</w>
-      <w>qrweibull</w>
-      <w>qsc</w>
-      <w>qseq</w>
-      <w>qsignrank</w>
-      <w>qsn</w>
-      <w>qsreg</w>
-      <w>qsreg.fit</w>
-      <w>qsreg.psi</w>
-      <w>qsreg.psi.OLD</w>
-      <w>qsreg.rho</w>
-      <w>qsreg.rho.OLD</w>
-      <w>qsreg.trace</w>
-      <w>qss</w>
-      <w>qss1</w>
-      <w>qss2</w>
-      <w>qst</w>
-      <w>qsubRun</w>
-      <w>qsurvreg</w>
-      <w>qsva</w>
-      <w>qt</w>
-      <w>qtukey</w>
-      <w>quade.test</w>
-      <w>quadprog</w>
-      <w>quadrant</w>
-      <w>quakes</w>
-      <w>qual</w>
-      <w>qualPath</w>
-      <w>qualitative_hcl</w>
-      <w>quality</w>
-      <w>qualityControl</w>
-      <w>qualitySubstitutionMatrices</w>
-      <w>quant.trans</w>
-      <w>quantcut</w>
-      <w>quantile</w>
-      <w>quantile.Rle</w>
-      <w>quantile.na</w>
-      <w>quantile.zoo</w>
-      <w>quantileMclust</w>
-      <w>quantilePositions</w>
-      <w>quantreg</w>
-      <w>quantregLine</w>
-      <w>quantro</w>
-      <w>quantroPlot</w>
-      <w>quantroPvalPerm</w>
-      <w>quantroStat</w>
-      <w>quantroStatPerm</w>
-      <w>quarter</w>
-      <w>quarters</w>
-      <w>quarters.Date</w>
-      <w>quarters.POSIXt</w>
-      <w>quartz</w>
-      <w>quartz.options</w>
-      <w>quartz.save</w>
-      <w>quartzFont</w>
-      <w>quartzFonts</w>
-      <w>quasi</w>
-      <w>quasibinomial</w>
-      <w>quasipoisson</w>
-      <w>query</w>
-      <w>queryHits</w>
-      <w>queryLength</w>
-      <w>queryLoc2refLoc</w>
-      <w>queryLocs2refLocs</w>
-      <w>queryRCmdCheck</w>
-      <w>queryRanges</w>
-      <w>querySeqs</w>
-      <w>quick.map</w>
-      <w>quickBamCounts</w>
-      <w>quickBamFlagSummary</w>
-      <w>quickCluster</w>
-      <w>quickCountBam</w>
-      <w>quickPrint</w>
-      <w>quickSummary</w>
-      <w>quickView</w>
-      <w>quickdf</w>
-      <w>quickinstall</w>
-      <w>quickload</w>
-      <w>quickorder</w>
-      <w>quickplot</w>
-      <w>quicksort</w>
-      <w>quicksortorder</w>
-      <w>quietgg</w>
-      <w>quietly</w>
-      <w>quilt.plot</w>
-      <w>quinModel</w>
-      <w>quine</w>
-      <w>quit</w>
-      <w>qunif</w>
-      <w>quo</w>
-      <w>quo_name</w>
-      <w>quos</w>
-      <w>quote</w>
-      <w>qvalue</w>
-      <w>qvalue.cal</w>
-      <w>qweibull</w>
-      <w>qwidth</w>
-      <w>qwilcox</w>
-      <w>r</w>
-      <w>r.con</w>
-      <w>r.norMix</w>
-      <w>r.test</w>
-      <w>r2c</w>
-      <w>r2chi</w>
-      <w>r2d</w>
-      <w>r2dtable</w>
-      <w>r2t</w>
-      <w>r6pack</w>
-      <w>rBind</w>
-      <w>rDNAbin</w>
-      <w>rFLXM</w>
-      <w>rFNCHypergeo</w>
-      <w>rFace</w>
-      <w>rMFNCHypergeo</w>
-      <w>rMWNCHypergeo</w>
-      <w>rMultinom</w>
-      <w>rSymmModulated</w>
-      <w>rToAffy</w>
-      <w>rToSymbol</w>
-      <w>rTraitCont</w>
-      <w>rTraitDisc</w>
-      <w>rTraitMult</w>
-      <w>rTweedie</w>
-      <w>rWNCHypergeo</w>
-      <w>rWishart</w>
-      <w>r_background</w>
-      <w>r_bg</w>
-      <w>r_copycat</w>
-      <w>r_env_vars</w>
-      <w>r_internal</w>
-      <w>r_pal</w>
-      <w>r_ply</w>
-      <w>r_process</w>
-      <w>r_process_options</w>
-      <w>r_safe</w>
-      <w>r_session</w>
-      <w>r_session_options</w>
-      <w>r_texmf</w>
-      <w>r_vanilla</w>
-      <w>r_wait</w>
-      <w>ra_ref</w>
-      <w>rabinerJuangStepPattern</w>
-      <w>radar</w>
-      <w>radarImage</w>
-      <w>radbas</w>
-      <w>radbas.constant</w>
-      <w>radial.grid</w>
-      <w>radial.pie</w>
-      <w>radial.plot</w>
-      <w>radial.plot.labels</w>
-      <w>radialtext</w>
-      <w>radioButtons</w>
-      <w>radius</w>
-      <w>radixorder</w>
-      <w>radixsort</w>
-      <w>radixsortorder</w>
-      <w>raftery.diag</w>
-      <w>rainbow</w>
-      <w>rainbow_hcl</w>
-      <w>raintest</w>
-      <w>raise.dendrogram</w>
-      <w>raise_to_power</w>
-      <w>ramorder</w>
-      <w>ramsort</w>
-      <w>ramsortorder</w>
-      <w>randProj</w>
-      <w>rand_bytes</w>
-      <w>rand_id</w>
-      <w>rand_num</w>
-      <w>rand_seed</w>
-      <w>randcmatrix</w>
-      <w>randconf</w>
-      <w>randinvvar</w>
-      <w>random.effects</w>
-      <w>random.graph.game</w>
-      <w>randomEGraph</w>
-      <w>randomGraph</w>
-      <w>randomGraphLayout</w>
-      <w>randomNodeGraph</w>
-      <w>randomPairs</w>
-      <w>random_walk</w>
-      <w>randomclustersim</w>
-      <w>randomizeRegions</w>
-      <w>randomize_regions</w>
-      <w>randomizedBlock</w>
-      <w>randomizedBlockFit</w>
-      <w>randomly</w>
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-      <w>randpop.nb</w>
-      <w>randu</w>
-      <w>ranef</w>
-      <w>range</w>
-      <w>range.bit</w>
-      <w>range.bitwhich</w>
-      <w>range.default</w>
-      <w>range.ri</w>
-      <w>range01</w>
-      <w>rangeComparisonCodeToLetter</w>
-      <w>rangeCorrection</w>
-      <w>rangeVal</w>
-      <w>ranger</w>
-      <w>ranges</w>
-      <w>rangeslider</w>
-      <w>rank</w>
-      <w>rankMM</w>
-      <w>rankMatrix</w>
-      <w>rankMembers</w>
-      <w>rankSeqlevels</w>
-      <w>rankSumTestWithCorrelation</w>
-      <w>rank_branches</w>
-      <w>rank_order.dendrogram</w>
-      <w>rank_values_with_clusters</w>
-      <w>ranking</w>
-      <w>rankinvariant</w>
-      <w>ranks</w>
-      <w>raply</w>
-      <w>rapply</w>
-      <w>raster</w>
-      <w>raster.from.asc</w>
-      <w>raster2uri</w>
-      <w>rasterFromCells</w>
-      <w>rasterFromXYZ</w>
-      <w>rasterGrob</w>
-      <w>rasterImage</w>
-      <w>rasterOptions</w>
-      <w>rasterTmpFile</w>
-      <w>rasterToContour</w>
-      <w>rasterToPoints</w>
-      <w>rasterToPolygons</w>
-      <w>rasterize</w>
-      <w>rat.diet</w>
-      <w>ratetable</w>
-      <w>ratetableDate</w>
-      <w>ratify</w>
-      <w>ratioConvert</w>
-      <w>rational</w>
-      <w>rats</w>
-      <w>rattr</w>
-      <w>raw</w>
-      <w>raw.means.plot</w>
-      <w>raw.means.plot2</w>
-      <w>rawConnection</w>
-      <w>rawConnectionValue</w>
-      <w>rawShift</w>
-      <w>rawToBase64</w>
-      <w>rawToBits</w>
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-      <w>raw_html</w>
-      <w>raw_latex</w>
-      <w>raw_output</w>
-      <w>raw_string</w>
-      <w>rawfd2dataf</w>
-      <w>razip</w>
-      <w>rbdtree</w>
-      <w>rbernoulli</w>
-      <w>rbeta</w>
-      <w>rbfdot</w>
-      <w>rbfox_genes</w>
-      <w>rbind</w>
-      <w>rbind.CompressedMatrix</w>
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-      <w>rbind.MAList</w>
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-      <w>rbind.SpatialLines</w>
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-      <w>rbind.SpatialPixels</w>
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-      <w>rbind.marrayInfo</w>
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-      <w>rbvhr</w>
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-      <w>rbvneglog</w>
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-      <w>rc.settings</w>
-      <w>rc.status</w>
-      <w>rcModelMedianPolish</w>
-      <w>rcModelPLM</w>
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-      <w>rcModelPLMr</w>
-      <w>rcModelPLMrc</w>
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-      <w>rcModelWPLM</w>
-      <w>rcModelWPLMr</w>
-      <w>rcModelWPLMrc</w>
-      <w>rcModelWPLMrr</w>
-      <w>rcauchy</w>
-      <w>rchisq</w>
-      <w>rcmd</w>
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-      <w>rcmd_build_tools</w>
-      <w>rcmd_copycat</w>
-      <w>rcmd_process</w>
-      <w>rcmd_process_options</w>
-      <w>rcmd_safe</w>
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-      <w>rcmdcheck</w>
-      <w>rcmdcheck_process</w>
-      <w>rcoal</w>
-      <w>rcond</w>
-      <w>rcor0</w>
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-      <w>rcpp</w>
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-      <w>rcur</w>
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-      <w>rdo_top_tags</w>
-      <w>rdply</w>
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-      <w>reLabelled</w>
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-      <w>re_match</w>
-      <w>reactive</w>
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-      <w>reactivePoll</w>
-      <w>reactivePrint</w>
-      <w>reactiveTable</w>
-      <w>reactiveText</w>
-      <w>reactiveTimer</w>
-      <w>reactiveUI</w>
-      <w>reactiveVal</w>
-      <w>reactiveValues</w>
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-      <w>reactlog</w>
-      <w>reactlogReset</w>
-      <w>reactlogShow</w>
-      <w>reactomeGS</w>
-      <w>reactomePathways</w>
-      <w>read</w>
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-      <w>read.450k</w>
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-      <w>read.450k.sheet</w>
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-      <w>read.HB</w>
-      <w>read.MIAME</w>
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-      <w>read.affybatch</w>
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-      <w>read.dbf</w>
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-      <w>read.fortran</w>
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-      <w>read.fwf</w>
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-      <w>read.gif</w>
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-      <w>read.idat</w>
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-      <w>read.liftMask</w>
-      <w>read.maimages</w>
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-      <w>read.matrix.csr</w>
-      <w>read.matrix.hb</w>
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-      <w>read.nexus</w>
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-      <w>read.octave</w>
-      <w>read.openbugs</w>
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-      <w>read.rmMask</w>
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-      <w>read.ssd</w>
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-      <w>read.umtab</w>
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-      <w>read.xls</w>
-      <w>read.xlsx</w>
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-      <w>read454</w>
-      <w>readAAMultipleAlignment</w>
-      <w>readAAStringSet</w>
-      <w>readAligned</w>
-      <w>readAll</w>
-      <w>readAncora</w>
-      <w>readAncoraIntoSQLite</w>
-      <w>readAsciiGrid</w>
-      <w>readAxt</w>
-      <w>readBGX</w>
-      <w>readBPM</w>
-      <w>readBStringSet</w>
-      <w>readBaseQuality</w>
-      <w>readBeadSummaryData</w>
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-      <w>readBfaToc</w>
-      <w>readBin</w>
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-      <w>readByte.Java</w>
-      <w>readCNERangesFromSQLite</w>
-      <w>readChar</w>
-      <w>readCitationFile</w>
-      <w>readComp</w>
-      <w>readCompressedData</w>
-      <w>readCount</w>
-      <w>readDGE</w>
-      <w>readDNAMultipleAlignment</w>
-      <w>readDNAStringSet</w>
-      <w>readData</w>
-      <w>readEPIC</w>
-      <w>readExpressionSet</w>
-      <w>readFasta</w>
-      <w>readFastaQual</w>
-      <w>readFastq</w>
-      <w>readGAL</w>
-      <w>readGAlignmentPairs</w>
-      <w>readGAlignments</w>
-      <w>readGAlignmentsList</w>
-      <w>readGEOAnn</w>
-      <w>readGEORawFile</w>
-      <w>readGFF</w>
-      <w>readGFFAsGRanges</w>
-      <w>readGFFPragmas</w>
-      <w>readGPRHeader</w>
-      <w>readGPS</w>
-      <w>readGT</w>
-      <w>readGappedReads</w>
-      <w>readGenericHeader</w>
-      <w>readGeno</w>
-      <w>readHB</w>
-      <w>readHTMLList</w>
-      <w>readHTMLTable</w>
-      <w>readIDAT</w>
-      <w>readIDNAcc</w>
-      <w>readIdatFiles</w>
-      <w>readIllumina</w>
-      <w>readImaGeneHeader</w>
-      <w>readIndex</w>
-      <w>readInfo</w>
-      <w>readIniFile</w>
-      <w>readInt</w>
-      <w>readInt.Java</w>
-      <w>readIntensities</w>
-      <w>readIntensityInfo</w>
-      <w>readKallisto</w>
-      <w>readKallistoBootstrap</w>
-      <w>readKallistoResults</w>
-      <w>readKallistoResultsOneSample</w>
-      <w>readKeyValueDB</w>
-      <w>readLines</w>
-      <w>readLocsFile</w>
-      <w>readMM</w>
-      <w>readMappings</w>
-      <w>readMetadataFromCsv</w>
-      <w>readMotifs</w>
-      <w>readNEWS</w>
-      <w>readPNG</w>
-      <w>readParam</w>
-      <w>readPath</w>
-      <w>readPeakFile</w>
-      <w>readPicture</w>
-      <w>readPileup</w>
-      <w>readPrb</w>
-      <w>readPreference</w>
-      <w>readQseq</w>
-      <w>readQual</w>
-      <w>readRDS</w>
-      <w>readRGB</w>
-      <w>readRNAMultipleAlignment</w>
-      <w>readRNAStringSet</w>
-      <w>readRdHelp</w>
-      <w>readRdHelp.default</w>
-      <w>readRenviron</w>
-      <w>readSAScsv</w>
-      <w>readSMDHeader</w>
-      <w>readSTARJunctions</w>
-      <w>readSalmonResults</w>
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-      <w>readSampleSheet</w>
-      <w>readShapeLines</w>
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-      <w>readShapePoly</w>
-      <w>readShapeSpatial</w>
-      <w>readShort</w>
-      <w>readShort.Java</w>
-      <w>readSolrDoc</w>
-      <w>readSplus</w>
-      <w>readSpotTypes</w>
-      <w>readStart</w>
-      <w>readStop</w>
-      <w>readTCGA</w>
-      <w>readTIFF</w>
-      <w>readTable</w>
-      <w>readTable.default</w>
-      <w>readTableIndex</w>
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-      <w>readTargets</w>
-      <w>readTopHatJunctions</w>
-      <w>readTxResults</w>
-      <w>readUTF</w>
-      <w>readUTF.Java</w>
-      <w>readUrl</w>
-      <w>readVcf</w>
-      <w>readVcfAsVRanges</w>
-      <w>readWindowsShellLink</w>
-      <w>readWindowsShellLink.default</w>
-      <w>readWindowsShortcut</w>
-      <w>readWindowsShortcut.default</w>
-      <w>readWorkbook</w>
-      <w>readXStringColumns</w>
-      <w>read_abatch</w>
-      <w>read_abatch_stddev</w>
-      <w>read_annotations</w>
-      <w>read_bytes</w>
-      <w>read_cert</w>
-      <w>read_cert_bundle</w>
-      <w>read_chunk</w>
-      <w>read_clip</w>
-      <w>read_clip_tbl</w>
-      <w>read_csv</w>
-      <w>read_csv2</w>
-      <w>read_csv2_chunked</w>
-      <w>read_csv_chunked</w>
-      <w>read_delim</w>
-      <w>read_delim_chunked</w>
-      <w>read_demo</w>
-      <w>read_dta</w>
-      <w>read_ed25519_key</w>
-      <w>read_ed25519_pubkey</w>
-      <w>read_excel</w>
-      <w>read_file</w>
-      <w>read_file_raw</w>
-      <w>read_fwf</w>
-      <w>read_graph</w>
-      <w>read_html</w>
-      <w>read_json</w>
-      <w>read_key</w>
-      <w>read_lines</w>
-      <w>read_lines_bytes</w>
-      <w>read_lines_chunked</w>
-      <w>read_lines_raw</w>
-      <w>read_lines_raw_chunked</w>
-      <w>read_log</w>
-      <w>read_p12</w>
-      <w>read_p7b</w>
-      <w>read_pem</w>
-      <w>read_por</w>
-      <w>read_pubkey</w>
-      <w>read_rds</w>
-      <w>read_rdump</w>
-      <w>read_regions</w>
-      <w>read_rforge</w>
-      <w>read_sas</w>
-      <w>read_sav</w>
-      <w>read_spss</w>
-      <w>read_stan_csv</w>
-      <w>read_stata</w>
-      <w>read_stm_CLUTO</w>
-      <w>read_stm_MC</w>
-      <w>read_table</w>
-      <w>read_table2</w>
-      <w>read_tsv</w>
-      <w>read_tsv_chunked</w>
-      <w>read_users</w>
-      <w>read_utf8</w>
-      <w>read_x25519_key</w>
-      <w>read_x25519_pubkey</w>
-      <w>read_xls</w>
-      <w>read_xlsx</w>
-      <w>read_xml</w>
-      <w>read_xpt</w>
-      <w>read_yaml</w>
-      <w>reader</w>
-      <w>readhex</w>
-      <w>readline</w>
-      <w>readr</w>
-      <w>readr_example</w>
-      <w>readxl</w>
-      <w>readxl_example</w>
-      <w>readxl_progress</w>
-      <w>realize</w>
-      <w>rearrange</w>
-      <w>reassignInPackage</w>
-      <w>reassignInPackage.default</w>
-      <w>rebib</w>
-      <w>recalc</w>
-      <w>recall</w>
-      <w>recast</w>
-      <w>recenter</w>
-      <w>rechunkByMargins</w>
-      <w>recipe</w>
-      <w>recipes</w>
-      <w>recipes_pkg_check</w>
-      <w>reciprocal_trans</w>
-      <w>reciprocity</w>
-      <w>reclass_date</w>
-      <w>reclass_timespan</w>
-      <w>reclassify</w>
-      <w>recode</w>
-      <w>recode_factor</w>
-      <w>recomputePermTest</w>
-      <w>reconcilePropertiesAndPrototype</w>
-      <w>reconst</w>
-      <w>reconstruct</w>
-      <w>reconstruction_error</w>
-      <w>reconstruction_rmse</w>
-      <w>recordGraphics</w>
-      <w>recordPlot</w>
-      <w>recordStatus</w>
-      <w>recover</w>
-      <w>rect</w>
-      <w>rect.dendrogram</w>
-      <w>rect.hclust</w>
-      <w>rect2polar</w>
-      <w>rectFill</w>
-      <w>rectGrob</w>
-      <w>rectangle.window</w>
-      <w>rectify</w>
-      <w>recurse</w>
-      <w>recvData</w>
-      <w>recvData.MPInode</w>
-      <w>recvData.NWSnode</w>
-      <w>recvData.SOCKnode</w>
-      <w>recvOneData</w>
-      <w>recvOneData.MPIcluster</w>
-      <w>recvOneData.NWScluster</w>
-      <w>recvOneData.SOCKcluster</w>
-      <w>recvOneResult</w>
-      <w>recvResult</w>
-      <w>recycleArg</w>
-      <w>recycleCharacterArg</w>
-      <w>recycleIntegerArg</w>
-      <w>recycleLogicalArg</w>
-      <w>recycleNumericArg</w>
-      <w>red</w>
-      <w>redChannelTransform</w>
-      <w>redblue</w>
-      <w>redgreen</w>
-      <w>redist</w>
-      <w>reduce</w>
-      <w>reduce.nn</w>
-      <w>reduce2</w>
-      <w>reduce2Degreek</w>
-      <w>reduce2_right</w>
-      <w>reduceResults</w>
-      <w>reduceResultsDataFrame</w>
-      <w>reduceResultsDataTable</w>
-      <w>reduceResultsList</w>
-      <w>reduceResultsMatrix</w>
-      <w>reduceResultsVector</w>
-      <w>reduce_right</w>
-      <w>reduce_simple_sparse_array</w>
-      <w>reducedDim</w>
-      <w>reducedDimNames</w>
-      <w>reducedDims</w>
-      <w>redun</w>
-      <w>ref</w>
-      <w>refDepth</w>
-      <w>refGenes</w>
-      <w>refdim</w>
-      <w>reference</w>
-      <w>referenceGenome</w>
-      <w>referenceQuantiles</w>
-      <w>referenceSequence</w>
-      <w>references</w>
-      <w>refit</w>
-      <w>refit_optim</w>
-      <w>reflect</w>
-      <w>reflog</w>
-      <w>reform</w>
-      <w>reformM</w>
-      <w>reformulate</w>
-      <w>reg.finalizer</w>
-      <w>regLine</w>
-      <w>regband</w>
-      <w>regcr</w>
-      <w>regem</w>
-      <w>regex</w>
-      <w>regexec</w>
-      <w>regexpr</w>
-      <w>regfetch</w>
-      <w>regfix</w>
-      <w>regionCounts</w>
-      <w>regionFinder</w>
-      <w>regioneR</w>
-      <w>register</w>
-      <w>registerCoresPWMEnrich</w>
-      <w>registerDoMC</w>
-      <w>registerDoParallel</w>
-      <w>registerDoRNG</w>
-      <w>registerDoSEQ</w>
-      <w>registerDoSNOW</w>
-      <w>registerImplicitGenerics</w>
-      <w>registerInputHandler</w>
-      <w>registerPlugin</w>
-      <w>registerS3method</w>
-      <w>registerS3methods</w>
-      <w>registered</w>
-      <w>registeredRenderers</w>
-      <w>registry</w>
-      <w>regmatches</w>
-      <w>regmix</w>
-      <w>regmix.init</w>
-      <w>regmix.lambda.init</w>
-      <w>regmix.mixed.init</w>
-      <w>regmixEM</w>
-      <w>regmixEM.lambda</w>
-      <w>regmixEM.loc</w>
-      <w>regmixEM.mixed</w>
-      <w>regmixMH</w>
-      <w>regmixmodel.sel</w>
-      <w>regpop.sar</w>
-      <w>regression</w>
-      <w>regroup</w>
-      <w>regsubsets</w>
-      <w>regtest.bit</w>
-      <w>regular_minor_breaks</w>
-      <w>regularization_term</w>
-      <w>reindex</w>
-      <w>reindex_clusters</w>
-      <w>reindex_dend</w>
-      <w>reinstall_tinytex</w>
-      <w>rejected_hypotheses</w>
-      <w>rejectionRate</w>
-      <w>rejection_plot</w>
-      <w>rejections</w>
-      <w>rel</w>
-      <w>relabel</w>
-      <w>relativeRanges</w>
-      <w>relative_eff</w>
-      <w>relative_to</w>
-      <w>release</w>
-      <w>releaseDate</w>
-      <w>releaseName</w>
-      <w>release_checks</w>
-      <w>relevel</w>
-      <w>relist</w>
-      <w>relistToClass</w>
-      <w>reload</w>
-      <w>reloadData</w>
-      <w>remapHits</w>
-      <w>rematch</w>
-      <w>rematchDefinition</w>
-      <w>remission</w>
-      <w>remlscore</w>
-      <w>remlscoregamma</w>
-      <w>remote</w>
-      <w>remote_add</w>
-      <w>remote_ls</w>
-      <w>remote_remove</w>
-      <w>remote_rename</w>
-      <w>remote_set_url</w>
-      <w>remote_url</w>
-      <w>remotes</w>
-      <w>remove</w>
-      <w>remove.args</w>
-      <w>remove.duplicates</w>
-      <w>remove.edge.attribute</w>
-      <w>remove.graph.attribute</w>
-      <w>remove.packages</w>
-      <w>remove.vars</w>
-      <w>remove.vertex.attribute</w>
-      <w>removeAttributes</w>
-      <w>removeBatchEffect</w>
-      <w>removeBeadData</w>
-      <w>removeCache</w>
-      <w>removeCellMerge</w>
-      <w>removeChildren</w>
-      <w>removeClass</w>
-      <w>removeColWidths</w>
-      <w>removeComment</w>
-      <w>removeCssClass</w>
-      <w>removeDirectory</w>
-      <w>removeDirectory.default</w>
-      <w>removeEdge</w>
-      <w>removeEdgesByWeight</w>
-      <w>removeExt</w>
-      <w>removeFilter</w>
-      <w>removeGeneric</w>
-      <w>removeGrob</w>
-      <w>removeInputHandler</w>
-      <w>removeMethod</w>
-      <w>removeMethods</w>
-      <w>removeMethodsObject</w>
-      <w>removeModal</w>
-      <w>removeNode</w>
-      <w>removeNodes</w>
-      <w>removeNotification</w>
-      <w>removeRegistry</w>
-      <w>removeRegistryPackages</w>
-      <w>removeRegistrySourceDirs</w>
-      <w>removeRegistrySourceFiles</w>
-      <w>removeResults</w>
-      <w>removeRowHeights</w>
-      <w>removeSelfLoops</w>
-      <w>removeSource</w>
-      <w>removeTab</w>
-      <w>removeTable</w>
-      <w>removeTaskCallback</w>
-      <w>removeTheme</w>
-      <w>removeTmpFiles</w>
-      <w>removeUI</w>
-      <w>removeWorksheet</w>
-      <w>removeXMLNamespaces</w>
-      <w>remove_branches_edgePar</w>
-      <w>remove_hooks</w>
-      <w>remove_leaves_nodePar</w>
-      <w>remove_missing</w>
-      <w>remove_nodes_nodePar</w>
-      <w>remove_role</w>
-      <w>remove_rownames</w>
-      <w>remove_typedarray_polyfill</w>
-      <w>removedEdges</w>
-      <w>rename</w>
-      <w>rename.vars</w>
-      <w>renameFile</w>
-      <w>renameFile.default</w>
-      <w>renameSeqlevels</w>
-      <w>renameWorksheet</w>
-      <w>rename_</w>
-      <w>rename_all</w>
-      <w>rename_at</w>
-      <w>rename_if</w>
-      <w>rename_vars</w>
-      <w>rename_vars_</w>
-      <w>render</w>
-      <w>renderCachedPlot</w>
-      <w>renderDT</w>
-      <w>renderDataTable</w>
-      <w>renderDependencies</w>
-      <w>renderDocument</w>
-      <w>renderDropdownMenu</w>
-      <w>renderGraph</w>
-      <w>renderHtmlTableWidget</w>
-      <w>renderImage</w>
-      <w>renderInfoBox</w>
-      <w>renderMarkdown</w>
-      <w>renderMenu</w>
-      <w>renderPlot</w>
-      <w>renderPlotly</w>
-      <w>renderPrint</w>
-      <w>renderTable</w>
-      <w>renderTags</w>
-      <w>renderText</w>
-      <w>renderUI</w>
-      <w>renderValueBox</w>
-      <w>render_asciidoc</w>
-      <w>render_axes</w>
-      <w>render_delayed</w>
-      <w>render_html</w>
-      <w>render_jekyll</w>
-      <w>render_latex</w>
-      <w>render_listings</w>
-      <w>render_markdown</w>
-      <w>render_notes</w>
-      <w>render_rst</w>
-      <w>render_site</w>
-      <w>render_strips</w>
-      <w>render_supporting_files</w>
-      <w>render_sweave</w>
-      <w>render_textile</w>
-      <w>rendererExists</w>
-      <w>rendererOutputType</w>
-      <w>renew</w>
-      <w>renewable</w>
-      <w>renumerate</w>
-      <w>reorder</w>
-      <w>reorder.evonet</w>
-      <w>reorder.factor</w>
-      <w>reorder.multiPhylo</w>
-      <w>reorder.phylo</w>
-      <w>reorderGrob</w>
-      <w>reorderRcpp</w>
-      <w>reorder_columns</w>
-      <w>rep</w>
-      <w>rep.Date</w>
-      <w>rep.POSIXct</w>
-      <w>rep.POSIXlt</w>
-      <w>rep.factor</w>
-      <w>rep.int</w>
-      <w>rep.numeric_version</w>
-      <w>rep2abI</w>
-      <w>repChar</w>
-      <w>rep_along</w>
-      <w>rep_len</w>
-      <w>repair_names</w>
-      <w>repeat.time</w>
-      <w>repeatable</w>
-      <w>repfromto</w>
-      <w>replace</w>
-      <w>replace.substring.wild</w>
-      <w>replaceAt</w>
-      <w>replaceData</w>
-      <w>replaceLetterAt</w>
-      <w>replaceNodes</w>
-      <w>replaceOutliers</w>
-      <w>replaceOutliersWithTrimmedMean</w>
-      <w>replaceROWS</w>
-      <w>replaceStyle</w>
-      <w>replace_na</w>
-      <w>replay</w>
-      <w>replayPlot</w>
-      <w>replicate</w>
-      <w>replicate.matrix</w>
-      <w>replicates</w>
-      <w>replications</w>
-      <w>repnormmix.init</w>
-      <w>repnormmixEM</w>
-      <w>repnormmixmodel.sel</w>
-      <w>report</w>
-      <w>report_html</w>
-      <w>reporter</w>
-      <w>repository</w>
-      <w>repository_head</w>
-      <w>representation</w>
-      <w>reprompt</w>
-      <w>req</w>
-      <w>require</w>
-      <w>require.quiet</w>
-      <w>requireMethods</w>
-      <w>requireNamespace</w>
-      <w>requirePackage</w>
-      <w>requirePackages</w>
-      <w>requireRUnit</w>
-      <w>rerequest</w>
-      <w>rerun</w>
-      <w>res</w>
-      <w>res_mn</w>
-      <w>resample</w>
-      <w>resample.default</w>
-      <w>resampleHist</w>
-      <w>resampleRegions</w>
-      <w>resampleSummary</w>
-      <w>resampleWrapper</w>
-      <w>resamples</w>
-      <w>resaveRdaFiles</w>
-      <w>rescale</w>
-      <w>rescale01</w>
-      <w>rescale11</w>
-      <w>rescale_max</w>
-      <w>rescale_mid</w>
-      <w>rescale_none</w>
-      <w>rescale_pal</w>
-      <w>reset</w>
-      <w>reset.ProgressBar</w>
-      <w>reset.SmartComments</w>
-      <w>reset.VComments</w>
-      <w>reset.options</w>
-      <w>resetClass</w>
-      <w>resetFilter</w>
-      <w>resetGeneric</w>
-      <w>resetJobs</w>
-      <w>resetOptions</w>
-      <w>resetOptions.character</w>
-      <w>resetOptions.default</w>
-      <w>resetPar</w>
-      <w>resetWarnings</w>
-      <w>resetWarnings.default</w>
-      <w>reset_config</w>
-      <w>resettest</w>
-      <w>reshape</w>
-      <w>reshape2</w>
-      <w>resid</w>
-      <w>resid.Krig</w>
-      <w>resid.psych</w>
-      <w>resid.rqss</w>
-      <w>residop</w>
-      <w>residplot</w>
-      <w>residualPlot</w>
-      <w>residualPlots</w>
-      <w>residuals</w>
-      <w>residuals.MArrayLM</w>
-      <w>residuals.gam</w>
-      <w>residuals.glm</w>
-      <w>residuals.lm</w>
-      <w>residuals.monoreg</w>
-      <w>residuals.mselm</w>
-      <w>residuals.nlrq</w>
-      <w>residuals.psych</w>
-      <w>residuals.selm</w>
-      <w>residuals.slm</w>
-      <w>resize</w>
-      <w>resizePanels</w>
-      <w>resolution</w>
-      <w>resolve</w>
-      <w>resolveDependencies</w>
-      <w>resolveHJust</w>
-      <w>resolveRasterSize</w>
-      <w>resolveVJust</w>
-      <w>resolve_output_format</w>
-      <w>resolved</w>
-      <w>resort_base</w>
-      <w>resource</w>
-      <w>respnames</w>
-      <w>response.frequencies</w>
-      <w>responseSummary</w>
-      <w>restartDescription</w>
-      <w>restartFormals</w>
-      <w>restartSession</w>
-      <w>restimate</w>
-      <w>restore</w>
-      <w>restoreInput</w>
-      <w>restorePreserveChunks</w>
-      <w>restoreSeqlevels</w>
-      <w>restore_raw_output</w>
-      <w>restrict</w>
-      <w>restrictToSNV</w>
-      <w>restrictionMatrix2model</w>
-      <w>restrictionMatrix2model.lm</w>
-      <w>restrictionMatrix2model.mer</w>
-      <w>restrictionMatrix2model.merMod</w>
-      <w>result</w>
-      <w>results</w>
-      <w>resultsNames</w>
-      <w>retinopathy</w>
-      <w>retracemem</w>
-      <w>return</w>
-      <w>returnCluster</w>
-      <w>returnFilterColumns</w>
-      <w>returnRPKM</w>
-      <w>returnValue</w>
-      <w>reuters</w>
-      <w>rev</w>
-      <w>rev.Rle</w>
-      <w>rev.default</w>
-      <w>rev.rlepack</w>
-      <w>rev.zoo</w>
-      <w>revElements</w>
-      <w>rev_check</w>
-      <w>revalue</w>
-      <w>revaxis</w>
-      <w>revdep</w>
-      <w>revdep_check</w>
-      <w>revdep_check_print_problems</w>
-      <w>revdep_check_reset</w>
-      <w>revdep_check_resume</w>
-      <w>revdep_check_save_summary</w>
-      <w>revdep_email</w>
-      <w>revdep_maintainers</w>
-      <w>revdiag</w>
-      <w>reverse</w>
-      <w>reverse.code</w>
-      <w>reverseArch</w>
-      <w>reverseCigar</w>
-      <w>reverseComplement</w>
-      <w>reverseEdgeDirections</w>
-      <w>reverseSplit</w>
-      <w>reverse_trans</w>
-      <w>reversed</w>
-      <w>revmap</w>
-      <w>revoke_all</w>
-      <w>revparse_single</w>
-      <w>reweightPred</w>
-      <w>rewire</w>
-      <w>rexp</w>
-      <w>rexpmix</w>
-      <w>rextreme</w>
-      <w>rf</w>
-      <w>rfFuncs</w>
-      <w>rfGA</w>
-      <w>rfSA</w>
-      <w>rfSBF</w>
-      <w>rfStats</w>
-      <w>rfe</w>
-      <w>rfeControl</w>
-      <w>rfeIter</w>
-      <w>rflexmix</w>
-      <w>rfpi</w>
-      <w>rfrechet</w>
-      <w>rfs</w>
-      <w>rgamma</w>
-      <w>rgb</w>
-      <w>rgb2hsv</w>
-      <w>rgb2mnsl</w>
-      <w>rgb_gsea</w>
-      <w>rgb_material</w>
-      <w>rgeom</w>
-      <w>rgeosStatus</w>
-      <w>rgev</w>
-      <w>rglist</w>
-      <w>rglplot</w>
-      <w>rgpd</w>
-      <w>rgumbel</w>
-      <w>rhDNase</w>
-      <w>rhalfnorm</w>
-      <w>rhdf5</w>
-      <w>rheMac2.ensGene.LENGTH</w>
-      <w>rheMac2.geneSymbol.LENGTH</w>
-      <w>rheMac2.geneid.LENGTH</w>
-      <w>rheMac2.nscanGene.LENGTH</w>
-      <w>rheMac2.refGene.LENGTH</w>
-      <w>rheMac2.sgpGene.LENGTH</w>
-      <w>rheMac2.xenoRefGene.LENGTH</w>
-      <w>rho</w>
-      <w>rhyper</w>
-      <w>ri</w>
-      <w>ribbon.plot</w>
-      <w>rice</w>
-      <w>rich.colors</w>
-      <w>richness.yule.test</w>
-      <w>rid</w>
-      <w>ridge</w>
-      <w>ridgeline</w>
-      <w>ridgeline.diagnosis</w>
-      <w>ridgeplot</w>
-      <w>rig</w>
-      <w>right</w>
-      <w>right_join</w>
-      <w>rigid</w>
-      <w>ring</w>
-      <w>rinvgamma</w>
-      <w>rinvgauss</w>
-      <w>rio</w>
-      <w>ripemd160</w>
-      <w>riskcomp</w>
-      <w>rivers</w>
-      <w>riwish</w>
-      <w>rjd</w>
-      <w>rjd.fortran</w>
-      <w>rjson</w>
-      <w>rl</w>
-      <w>rlatin</w>
-      <w>rle</w>
-      <w>rlegend</w>
-      <w>rlegendg</w>
-      <w>rleid</w>
-      <w>rleidv</w>
-      <w>rlepack</w>
-      <w>rlepack.integer</w>
-      <w>rleunpack</w>
-      <w>rleunpack.rlepack</w>
-      <w>rlineage</w>
-      <w>rlm</w>
-      <w>rlnorm</w>
-      <w>rlog</w>
-      <w>rlogTransformation</w>
-      <w>rlogis</w>
-      <w>rlply</w>
-      <w>rm</w>
-      <w>rm.boot</w>
-      <w>rm.na</w>
-      <w>rmSNPandCH</w>
-      <w>rmSymmModulated</w>
-      <w>rm_file</w>
-      <w>rma</w>
-      <w>rma.background.correct</w>
-      <w>rmarkdown</w>
-      <w>rmarkdown_format</w>
-      <w>rmnorm</w>
-      <w>rms.curv</w>
-      <w>rms.wavefront</w>
-      <w>rmsc</w>
-      <w>rmse</w>
-      <w>rmsle</w>
-      <w>rmsn</w>
-      <w>rmssd</w>
-      <w>rmst</w>
-      <w>rmt</w>
-      <w>rmtree</w>
-      <w>rmultinom</w>
-      <w>rmultinomial</w>
-      <w>rmultz2</w>
-      <w>rmvalog</w>
-      <w>rmvar</w>
-      <w>rmvevd</w>
-      <w>rmvlog</w>
-      <w>rmvn</w>
-      <w>rmvn0</w>
-      <w>rmvnorm</w>
-      <w>rmvnorm.canonical</w>
-      <w>rmvnorm.canonical.const</w>
-      <w>rmvnorm.const</w>
-      <w>rmvnorm.prec</w>
-      <w>rmvnorm.prec.const</w>
-      <w>rmvnorm.spam</w>
-      <w>rmvnormmix</w>
-      <w>rmvt</w>
-      <w>rn3.ensGene.LENGTH</w>
-      <w>rn3.geneSymbol.LENGTH</w>
-      <w>rn3.geneid.LENGTH</w>
-      <w>rn3.genscan.LENGTH</w>
-      <w>rn3.knownGene.LENGTH</w>
-      <w>rn3.nscanGene.LENGTH</w>
-      <w>rn3.refGene.LENGTH</w>
-      <w>rn3.sgpGene.LENGTH</w>
-      <w>rn3.xenoRefGene.LENGTH</w>
-      <w>rn4.ensGene.LENGTH</w>
-      <w>rn4.geneSymbol.LENGTH</w>
-      <w>rn4.geneid.LENGTH</w>
-      <w>rn4.genscan.LENGTH</w>
-      <w>rn4.knownGene.LENGTH</w>
-      <w>rn4.nscanGene.LENGTH</w>
-      <w>rn4.refGene.LENGTH</w>
-      <w>rn4.sgpGene.LENGTH</w>
-      <w>rn4.xenoRefGene.LENGTH</w>
-      <w>rname</w>
-      <w>rnbinom</w>
-      <w>rnegbin</w>
-      <w>rng.equal</w>
-      <w>rng1.equal</w>
-      <w>rngtools</w>
-      <w>rnoncenhypergeom</w>
-      <w>rnorMix</w>
-      <w>rnorm</w>
-      <w>rnormmix</w>
-      <w>rnw</w>
-      <w>rnwChildren</w>
-      <w>rnwCompiler</w>
-      <w>rnwDriver</w>
-      <w>rnwIncludes</w>
-      <w>rnwWrapper</w>
-      <w>rnweibull</w>
-      <w>road</w>
-      <w>roast</w>
-      <w>roast.DGEList</w>
-      <w>roast.default</w>
-      <w>robMD</w>
-      <w>robustQuantileNorm_Illumina450K</w>
-      <w>robustQuantileNorm_Illumina450K.probeCategories</w>
-      <w>robustbase</w>
-      <w>rocco</w>
-      <w>rocdemo.sca</w>
-      <w>rock</w>
-      <w>roll_max</w>
-      <w>roll_maxl</w>
-      <w>roll_maxr</w>
-      <w>roll_mean</w>
-      <w>roll_meanl</w>
-      <w>roll_meanr</w>
-      <w>roll_median</w>
-      <w>roll_medianl</w>
-      <w>roll_medianr</w>
-      <w>roll_min</w>
-      <w>roll_minl</w>
-      <w>roll_minr</w>
-      <w>roll_prod</w>
-      <w>roll_prodl</w>
-      <w>roll_prodr</w>
-      <w>roll_sd</w>
-      <w>roll_sdl</w>
-      <w>roll_sdr</w>
-      <w>roll_sum</w>
-      <w>roll_suml</w>
-      <w>roll_sumr</w>
-      <w>roll_var</w>
-      <w>roll_varl</w>
-      <w>roll_varr</w>
-      <w>rollapply</w>
-      <w>rollapplyr</w>
-      <w>rollback</w>
-      <w>rollmax</w>
-      <w>rollmax.default</w>
-      <w>rollmaxr</w>
-      <w>rollmean</w>
-      <w>rollmean.default</w>
-      <w>rollmeanr</w>
-      <w>rollmedian</w>
-      <w>rollmedian.default</w>
-      <w>rollmedianr</w>
-      <w>rollsum</w>
-      <w>rollsum.default</w>
-      <w>rollsumr</w>
-      <w>rollup</w>
-      <w>roman2int</w>
-      <w>romer</w>
-      <w>romer.DGEList</w>
-      <w>romer.default</w>
-      <w>root</w>
-      <w>root.multiPhylo</w>
-      <w>root.phylo</w>
-      <w>root_criterion</w>
-      <w>rootogram</w>
-      <w>roots</w>
-      <w>rorder</w>
-      <w>rosenthal</w>
-      <w>rot2</w>
-      <w>rot2D</w>
-      <w>rot3D</w>
-      <w>rotate</w>
-      <w>rotate.sp</w>
-      <w>rotate.venn.degrees</w>
-      <w>rotate2</w>
-      <w>rotateConstr</w>
-      <w>rotate_DendSer</w>
-      <w>rotate_x_text</w>
-      <w>rotate_y_text</w>
-      <w>rotated</w>
-      <w>rotifer</w>
-      <w>rotn</w>
-      <w>round</w>
-      <w>round.Date</w>
-      <w>round.POSIXt</w>
-      <w>roundN</w>
-      <w>roundPOSIXt</w>
-      <w>round_any</w>
-      <w>round_date</w>
-      <w>round_hms</w>
-      <w>roundfixS</w>
-      <w>roundrectGrob</w>
-      <w>row</w>
-      <w>row.dist</w>
-      <w>row.match</w>
-      <w>row.names</w>
-      <w>row.names.data.frame</w>
-      <w>row.names.default</w>
-      <w>rowAlls</w>
-      <w>rowAnyMissings</w>
-      <w>rowAnyNAs</w>
-      <w>rowAnys</w>
-      <w>rowAvgsPerColSet</w>
-      <w>rowColFromCell</w>
-      <w>rowCollapse</w>
-      <w>rowCounts</w>
-      <w>rowCummaxs</w>
-      <w>rowCummins</w>
-      <w>rowCumprods</w>
-      <w>rowCumsums</w>
-      <w>rowData</w>
-      <w>rowDiffs</w>
-      <w>rowFromCell</w>
-      <w>rowFromY</w>
-      <w>rowFtests</w>
-      <w>rowIQRDiffs</w>
-      <w>rowIQRs</w>
-      <w>rowLapply</w>
-      <w>rowLogSumExps</w>
-      <w>rowMadDiffs</w>
-      <w>rowMads</w>
-      <w>rowMax</w>
-      <w>rowMaxs</w>
-      <w>rowMeans</w>
-      <w>rowMeans.dist</w>
-      <w>rowMeans.spam</w>
-      <w>rowMeans2</w>
-      <w>rowMedians</w>
-      <w>rowMin</w>
-      <w>rowMins</w>
-      <w>rowOrderStats</w>
-      <w>rowProds</w>
-      <w>rowQ</w>
-      <w>rowQuantiles</w>
-      <w>rowRanges</w>
-      <w>rowRanks</w>
-      <w>rowRanksWilc</w>
-      <w>rowSapply</w>
-      <w>rowSdDiffs</w>
-      <w>rowSds</w>
-      <w>rowSplit</w>
-      <w>rowSums</w>
-      <w>rowSums.dist</w>
-      <w>rowSums.spam</w>
-      <w>rowSums2</w>
-      <w>rowTabulates</w>
-      <w>rowVarDiffs</w>
-      <w>rowVars</w>
-      <w>rowWeightedMads</w>
-      <w>rowWeightedMeans</w>
-      <w>rowWeightedMedians</w>
-      <w>rowWeightedSds</w>
-      <w>rowWeightedVars</w>
-      <w>rowWilcoxon</w>
-      <w>row_means</w>
-      <w>row_norms</w>
-      <w>row_number</w>
-      <w>row_sums</w>
-      <w>rowapply_simple_triplet_matrix</w>
-      <w>rowid</w>
-      <w>rowid_to_column</w>
-      <w>rowids</w>
-      <w>rowidv</w>
-      <w>rowmask</w>
-      <w>rownames</w>
-      <w>rownames_style</w>
-      <w>rownames_to_column</w>
-      <w>rowpAUCs</w>
-      <w>rowsum</w>
-      <w>rowsum.DGEList</w>
-      <w>rowsum.data.frame</w>
-      <w>rowsum.default</w>
-      <w>rowttests</w>
-      <w>rowwise</w>
-      <w>rpart</w>
-      <w>rpart.control</w>
-      <w>rpart.exp</w>
-      <w>rpca</w>
-      <w>rphylo</w>
-      <w>rpkm</w>
-      <w>rpkm.DGEList</w>
-      <w>rpkm.default</w>
-      <w>rpkmByGroup</w>
-      <w>rpkmByGroup.DGEList</w>
-      <w>rpkmByGroup.default</w>
-      <w>rplcon</w>
-      <w>rpldis</w>
-      <w>rpois</w>
-      <w>rpretty</w>
-      <w>rprojroot</w>
-      <w>rpubsUpload</w>
-      <w>rq</w>
-      <w>rq.fit</w>
-      <w>rq.fit.br</w>
-      <w>rq.fit.fnb</w>
-      <w>rq.fit.fnc</w>
-      <w>rq.fit.hogg</w>
-      <w>rq.fit.lasso</w>
-      <w>rq.fit.pfn</w>
-      <w>rq.fit.scad</w>
-      <w>rq.fit.sfn</w>
-      <w>rq.fit.sfnc</w>
-      <w>rq.test.anowar</w>
-      <w>rq.test.rank</w>
-      <w>rq.wfit</w>
-      <w>rqProcess</w>
-      <w>rqb</w>
-      <w>rqs.fit</w>
-      <w>rqss</w>
-      <w>rqss.fit</w>
-      <w>rrange</w>
-      <w>rrcov</w>
-      <w>rrcov.control</w>
-      <w>rremove</w>
-      <w>rrpca</w>
-      <w>rrweibull</w>
-      <w>rsa_decrypt</w>
-      <w>rsa_encrypt</w>
-      <w>rsa_keygen</w>
-      <w>rsc</w>
-      <w>rscript</w>
-      <w>rscript_process</w>
-      <w>rscript_process_options</w>
-      <w>rsignrank</w>
-      <w>rsn</w>
-      <w>rsnps</w>
-      <w>rsnpsCache</w>
-      <w>rsparsematrix</w>
-      <w>rsq</w>
-      <w>rsq.rpart</w>
-      <w>rsqliteVersion</w>
-      <w>rst</w>
-      <w>rst2pdf</w>
-      <w>rstan</w>
-      <w>rstan.package.skeleton</w>
-      <w>rstan_gg_options</w>
-      <w>rstan_ggtheme_options</w>
-      <w>rstan_options</w>
-      <w>rstan_package_skeleton</w>
-      <w>rstandard</w>
-      <w>rstantools</w>
-      <w>rstudent</w>
-      <w>rstudio_type</w>
-      <w>rstudioapi</w>
-      <w>rsurv</w>
-      <w>rsurvreg</w>
-      <w>rsvd</w>
-      <w>rt</w>
-      <w>rtPCR</w>
-      <w>rtags</w>
-      <w>rtf_document</w>
-      <w>rtime</w>
-      <w>rtools_path</w>
-      <w>rtracklayer</w>
-      <w>rtree</w>
-      <w>rtt</w>
-      <w>rug</w>
-      <w>ruginv</w>
-      <w>rule</w>
-      <w>ruler</w>
-      <w>ruler.NullVerbose</w>
-      <w>ruler.Verbose</w>
-      <w>rulesFinCenter</w>
-      <w>run</w>
-      <w>runApp</w>
-      <w>runCommandline</w>
-      <w>runDiff</w>
-      <w>runDiffusionMap</w>
-      <w>runEnrichmentAnalysis</w>
-      <w>runEnsDbApp</w>
-      <w>runExample</w>
-      <w>runGadget</w>
-      <w>runGist</w>
-      <w>runGitHub</w>
-      <w>runKallisto</w>
-      <w>runLength</w>
-      <w>runMOFA</w>
-      <w>runMPIslave</w>
-      <w>runNames</w>
-      <w>runPCA</w>
-      <w>runPostponedAction</w>
-      <w>runSalmon</w>
-      <w>runServer</w>
-      <w>runTSNE</w>
-      <w>runTest</w>
-      <w>runTestFile</w>
-      <w>runTestSuite</w>
-      <w>runUrl</w>
-      <w>runValue</w>
-      <w>run_DESeq2</w>
-      <w>run_edgeR</w>
-      <w>run_example</w>
-      <w>run_examples</w>
-      <w>run_now</w>
-      <w>runcodeServer</w>
-      <w>runcodeUI</w>
-      <w>runif</w>
-      <w>runjs</w>
-      <w>runmad</w>
-      <w>runmax</w>
-      <w>runmean</w>
-      <w>runmed</w>
-      <w>runmedByCluster</w>
-      <w>runmin</w>
-      <w>running</w>
-      <w>running.mean</w>
-      <w>running_mean</w>
-      <w>runq</w>
-      <w>runquantile</w>
-      <w>runsd</w>
-      <w>runsum</w>
-      <w>runwtsum</w>
-      <w>ruspini</w>
-      <w>ruv</w>
-      <w>ruv_cancorplot</w>
-      <w>ruv_ecdf</w>
-      <w>ruv_hist</w>
-      <w>ruv_projectionplot</w>
-      <w>ruv_rankplot</w>
-      <w>ruv_residuals</w>
-      <w>ruv_rle</w>
-      <w>ruv_scree</w>
-      <w>ruv_shiny</w>
-      <w>ruv_summary</w>
-      <w>ruv_svdgridplot</w>
-      <w>ruv_svdplot</w>
-      <w>ruv_varianceplot</w>
-      <w>ruv_volcano</w>
-      <w>rv</w>
-      <w>rvcheck</w>
-      <w>rvm</w>
-      <w>rweibull</w>
-      <w>rweibullmix</w>
-      <w>rwiener</w>
-      <w>rwilcox</w>
-      <w>rwish</w>
-      <w>rygbp</w>
-      <w>s</w>
-      <w>s3_register</w>
-      <w>sHalton</w>
-      <w>sKey</w>
-      <w>sPCAgrid</w>
-      <w>sQuote</w>
-      <w>sRGB</w>
-      <w>sVariable</w>
-      <w>s_IQR</w>
-      <w>s_Qn</w>
-      <w>s_Sn</w>
-      <w>s_mad</w>
-      <w>sacCer1.ensGene.LENGTH</w>
-      <w>sacCer2.ensGene.LENGTH</w>
-      <w>saddle</w>
-      <w>saddle.distn</w>
-      <w>sadmvn</w>
-      <w>sadmvt</w>
-      <w>safeError</w>
-      <w>safeExplode</w>
-      <w>safe_median</w>
-      <w>safely</w>
-      <w>safs</w>
-      <w>safsControl</w>
-      <w>safs_initial</w>
-      <w>safs_perturb</w>
-      <w>safs_prob</w>
-      <w>sage.test</w>
-      <w>sagmbAssess</w>
-      <w>sagmbSimulateData</w>
-      <w>sai</w>
-      <w>sai.dictionary</w>
-      <w>sakoeChibaWindow</w>
-      <w>salinity</w>
-      <w>salmon</w>
-      <w>salmonellaTA98</w>
-      <w>sam</w>
-      <w>sam.plot2</w>
-      <w>sam2excel</w>
-      <w>sam2html</w>
-      <w>samControl</w>
-      <w>same.component</w>
-      <w>same_path</w>
-      <w>same_src</w>
-      <w>sammon</w>
-      <w>sample</w>
-      <w>sample.ExpressionSet</w>
-      <w>sample.MultiSet</w>
-      <w>sample.dendrogram</w>
-      <w>sample.int</w>
-      <w>sample.split</w>
-      <w>sampleInt</w>
-      <w>sampleLabels</w>
-      <w>sampleMap</w>
-      <w>sampleNAs</w>
-      <w>sampleNames</w>
-      <w>sampleRandom</w>
-      <w>sampleRegular</w>
-      <w>sampleStratified</w>
-      <w>sample_</w>
-      <w>sample_asym_pref</w>
-      <w>sample_bipartite</w>
-      <w>sample_cit_cit_types</w>
-      <w>sample_cit_types</w>
-      <w>sample_correlated_gnp</w>
-      <w>sample_correlated_gnp_pair</w>
-      <w>sample_degseq</w>
-      <w>sample_dirichlet</w>
-      <w>sample_dot_product</w>
-      <w>sample_fitness</w>
-      <w>sample_fitness_pl</w>
-      <w>sample_forestfire</w>
-      <w>sample_frac</w>
-      <w>sample_gnm</w>
-      <w>sample_gnp</w>
-      <w>sample_grg</w>
-      <w>sample_growing</w>
-      <w>sample_hierarchical_sbm</w>
-      <w>sample_hrg</w>
-      <w>sample_islands</w>
-      <w>sample_k_regular</w>
-      <w>sample_last_cit</w>
-      <w>sample_motifs</w>
-      <w>sample_n</w>
-      <w>sample_pa</w>
-      <w>sample_pa_age</w>
-      <w>sample_pref</w>
-      <w>sample_sbm</w>
-      <w>sample_seq</w>
-      <w>sample_smallworld</w>
-      <w>sample_sphere_surface</w>
-      <w>sample_sphere_volume</w>
-      <w>sample_traits</w>
-      <w>sample_traits_callaway</w>
-      <w>samples</w>
-      <w>samplesize.bin</w>
-      <w>sampling</w>
-      <w>sandbag</w>
-      <w>sanitize</w>
-      <w>sanitize.final</w>
-      <w>sanitize.numbers</w>
-      <w>sanitizePath</w>
-      <w>sans_ext</w>
-      <w>sapply</w>
-      <w>sas.codes</w>
-      <w>sas.get</w>
-      <w>sas.get.macro</w>
-      <w>sasdsLabels</w>
-      <w>sask</w>
-      <w>sasxport.get</w>
-      <w>sat.act</w>
-      <w>saturate</w>
-      <w>save</w>
-      <w>save.Object</w>
-      <w>save.default</w>
-      <w>save.image</w>
-      <w>save2</w>
-      <w>saveAnywhere</w>
-      <w>saveAnywhere.Settings</w>
-      <w>saveAsOnDiskLongTable_old</w>
-      <w>saveCNEToSQLite</w>
-      <w>saveDb</w>
-      <w>saveHDF5SummarizedExperiment</w>
-      <w>saveObject</w>
-      <w>saveObject.default</w>
-      <w>savePlot</w>
-      <w>savePlotAsImage</w>
-      <w>saveRDS</w>
-      <w>saveRowidsForOnDiskLongTable_old</w>
-      <w>saveWidget</w>
-      <w>saveWorkbook</w>
-      <w>saveXML</w>
-      <w>saveXStringSet</w>
-      <w>save_html</w>
-      <w>save_plot</w>
-      <w>saveeps</w>
-      <w>savehistory</w>
-      <w>savepdf</w>
-      <w>savepng</w>
-      <w>savetiff</w>
-      <w>sbf</w>
-      <w>sbfControl</w>
-      <w>sbfIter</w>
-      <w>sbm</w>
-      <w>sbm.game</w>
-      <w>sbplx</w>
-      <w>sbrier</w>
-      <w>sc3</w>
-      <w>sc3_calc_biology</w>
-      <w>sc3_calc_consens</w>
-      <w>sc3_calc_dists</w>
-      <w>sc3_calc_transfs</w>
-      <w>sc3_estimate_k</w>
-      <w>sc3_export_results_xls</w>
-      <w>sc3_interactive</w>
-      <w>sc3_kmeans</w>
-      <w>sc3_plot_cluster_stability</w>
-      <w>sc3_plot_consensus</w>
-      <w>sc3_plot_de_genes</w>
-      <w>sc3_plot_expression</w>
-      <w>sc3_plot_markers</w>
-      <w>sc3_plot_silhouette</w>
-      <w>sc3_prepare</w>
-      <w>sc3_run_svm</w>
-      <w>scBio</w>
-      <w>scMT_data</w>
-      <w>sc_example_cell_info</w>
-      <w>sc_example_counts</w>
-      <w>scaffoldWidget</w>
-      <w>scale</w>
-      <w>scale.default</w>
-      <w>scale.na</w>
-      <w>scaleControlFilter</w>
-      <w>scaleNodeColor</w>
-      <w>scaleOffset</w>
-      <w>scaleOffset.DGEList</w>
-      <w>scaleOffset.default</w>
-      <w>scaleRanges</w>
-      <w>scaleTau2</w>
-      <w>scale_alpha</w>
-      <w>scale_alpha_continuous</w>
-      <w>scale_alpha_cyclical</w>
-      <w>scale_alpha_date</w>
-      <w>scale_alpha_datetime</w>
-      <w>scale_alpha_discrete</w>
-      <w>scale_alpha_identity</w>
-      <w>scale_alpha_manual</w>
-      <w>scale_alpha_ordinal</w>
-      <w>scale_color_aaas</w>
-      <w>scale_color_brewer</w>
-      <w>scale_color_continuous</w>
-      <w>scale_color_continuous_diverging</w>
-      <w>scale_color_continuous_divergingx</w>
-      <w>scale_color_continuous_qualitative</w>
-      <w>scale_color_continuous_sequential</w>
-      <w>scale_color_cyclical</w>
-      <w>scale_color_d3</w>
-      <w>scale_color_discrete</w>
-      <w>scale_color_discrete_diverging</w>
-      <w>scale_color_discrete_divergingx</w>
-      <w>scale_color_discrete_qualitative</w>
-      <w>scale_color_discrete_sequential</w>
-      <w>scale_color_distiller</w>
-      <w>scale_color_futurama</w>
-      <w>scale_color_gradient</w>
-      <w>scale_color_gradient2</w>
-      <w>scale_color_gradientn</w>
-      <w>scale_color_grey</w>
-      <w>scale_color_gsea</w>
-      <w>scale_color_hue</w>
-      <w>scale_color_identity</w>
-      <w>scale_color_igv</w>
-      <w>scale_color_jama</w>
-      <w>scale_color_jco</w>
-      <w>scale_color_lancet</w>
-      <w>scale_color_locuszoom</w>
-      <w>scale_color_manual</w>
-      <w>scale_color_material</w>
-      <w>scale_color_nejm</w>
-      <w>scale_color_npg</w>
-      <w>scale_color_rickandmorty</w>
-      <w>scale_color_selection</w>
-      <w>scale_color_simpsons</w>
-      <w>scale_color_startrek</w>
-      <w>scale_color_tron</w>
-      <w>scale_color_uchicago</w>
-      <w>scale_color_ucscgb</w>
-      <w>scale_color_viridis</w>
-      <w>scale_color_viridis_c</w>
-      <w>scale_color_viridis_d</w>
-      <w>scale_colour_aaas</w>
-      <w>scale_colour_brewer</w>
-      <w>scale_colour_continuous</w>
-      <w>scale_colour_continuous_diverging</w>
-      <w>scale_colour_continuous_divergingx</w>
-      <w>scale_colour_continuous_qualitative</w>
-      <w>scale_colour_continuous_sequential</w>
-      <w>scale_colour_cyclical</w>
-      <w>scale_colour_d3</w>
-      <w>scale_colour_date</w>
-      <w>scale_colour_datetime</w>
-      <w>scale_colour_discrete</w>
-      <w>scale_colour_discrete_diverging</w>
-      <w>scale_colour_discrete_divergingx</w>
-      <w>scale_colour_discrete_qualitative</w>
-      <w>scale_colour_discrete_sequential</w>
-      <w>scale_colour_distiller</w>
-      <w>scale_colour_futurama</w>
-      <w>scale_colour_gradient</w>
-      <w>scale_colour_gradient2</w>
-      <w>scale_colour_gradientn</w>
-      <w>scale_colour_grey</w>
-      <w>scale_colour_gsea</w>
-      <w>scale_colour_hue</w>
-      <w>scale_colour_identity</w>
-      <w>scale_colour_igv</w>
-      <w>scale_colour_jama</w>
-      <w>scale_colour_jco</w>
-      <w>scale_colour_lancet</w>
-      <w>scale_colour_locuszoom</w>
-      <w>scale_colour_manual</w>
-      <w>scale_colour_material</w>
-      <w>scale_colour_nejm</w>
-      <w>scale_colour_npg</w>
-      <w>scale_colour_ordinal</w>
-      <w>scale_colour_rickandmorty</w>
-      <w>scale_colour_simpsons</w>
-      <w>scale_colour_startrek</w>
-      <w>scale_colour_tron</w>
-      <w>scale_colour_uchicago</w>
-      <w>scale_colour_ucscgb</w>
-      <w>scale_colour_viridis</w>
-      <w>scale_colour_viridis_c</w>
-      <w>scale_colour_viridis_d</w>
-      <w>scale_continuous_identity</w>
-      <w>scale_discrete_identity</w>
-      <w>scale_discrete_manual</w>
-      <w>scale_fill_aaas</w>
-      <w>scale_fill_brewer</w>
-      <w>scale_fill_continuous</w>
-      <w>scale_fill_continuous_diverging</w>
-      <w>scale_fill_continuous_divergingx</w>
-      <w>scale_fill_continuous_qualitative</w>
-      <w>scale_fill_continuous_sequential</w>
-      <w>scale_fill_cyclical</w>
-      <w>scale_fill_d3</w>
-      <w>scale_fill_date</w>
-      <w>scale_fill_datetime</w>
-      <w>scale_fill_discrete</w>
-      <w>scale_fill_discrete_diverging</w>
-      <w>scale_fill_discrete_divergingx</w>
-      <w>scale_fill_discrete_qualitative</w>
-      <w>scale_fill_discrete_sequential</w>
-      <w>scale_fill_distiller</w>
-      <w>scale_fill_futurama</w>
-      <w>scale_fill_gradient</w>
-      <w>scale_fill_gradient2</w>
-      <w>scale_fill_gradientn</w>
-      <w>scale_fill_grey</w>
-      <w>scale_fill_gsea</w>
-      <w>scale_fill_hue</w>
-      <w>scale_fill_identity</w>
-      <w>scale_fill_igv</w>
-      <w>scale_fill_jama</w>
-      <w>scale_fill_jco</w>
-      <w>scale_fill_lancet</w>
-      <w>scale_fill_locuszoom</w>
-      <w>scale_fill_manual</w>
-      <w>scale_fill_material</w>
-      <w>scale_fill_nejm</w>
-      <w>scale_fill_npg</w>
-      <w>scale_fill_ordinal</w>
-      <w>scale_fill_rickandmorty</w>
-      <w>scale_fill_selection</w>
-      <w>scale_fill_simpsons</w>
-      <w>scale_fill_startrek</w>
-      <w>scale_fill_tron</w>
-      <w>scale_fill_uchicago</w>
-      <w>scale_fill_ucscgb</w>
-      <w>scale_fill_viridis</w>
-      <w>scale_fill_viridis_c</w>
-      <w>scale_fill_viridis_d</w>
-      <w>scale_linetype</w>
-      <w>scale_linetype_continuous</w>
-      <w>scale_linetype_cyclical</w>
-      <w>scale_linetype_discrete</w>
-      <w>scale_linetype_identity</w>
-      <w>scale_linetype_manual</w>
-      <w>scale_point_color_continuous</w>
-      <w>scale_point_color_discrete</w>
-      <w>scale_point_color_gradient</w>
-      <w>scale_point_color_hue</w>
-      <w>scale_point_colour_continuous</w>
-      <w>scale_point_colour_discrete</w>
-      <w>scale_point_colour_gradient</w>
-      <w>scale_point_colour_hue</w>
-      <w>scale_point_fill_continuous</w>
-      <w>scale_point_fill_discrete</w>
-      <w>scale_point_fill_gradient</w>
-      <w>scale_point_fill_hue</w>
-      <w>scale_point_shape</w>
-      <w>scale_point_shape_discrete</w>
-      <w>scale_point_size_continuous</w>
-      <w>scale_radius</w>
-      <w>scale_shape</w>
-      <w>scale_shape_continuous</w>
-      <w>scale_shape_discrete</w>
-      <w>scale_shape_identity</w>
-      <w>scale_shape_manual</w>
-      <w>scale_shape_ordinal</w>
-      <w>scale_size</w>
-      <w>scale_size_area</w>
-      <w>scale_size_continuous</w>
-      <w>scale_size_cyclical</w>
-      <w>scale_size_date</w>
-      <w>scale_size_datetime</w>
-      <w>scale_size_discrete</w>
-      <w>scale_size_identity</w>
-      <w>scale_size_manual</w>
-      <w>scale_size_ordinal</w>
-      <w>scale_type</w>
-      <w>scale_vline_color_continuous</w>
-      <w>scale_vline_color_discrete</w>
-      <w>scale_vline_color_gradient</w>
-      <w>scale_vline_color_hue</w>
-      <w>scale_vline_colour_continuous</w>
-      <w>scale_vline_colour_discrete</w>
-      <w>scale_vline_colour_gradient</w>
-      <w>scale_vline_colour_hue</w>
-      <w>scale_vline_linetype</w>
-      <w>scale_vline_linetype_discrete</w>
-      <w>scale_vline_size_continuous</w>
-      <w>scale_x_continuous</w>
-      <w>scale_x_date</w>
-      <w>scale_x_datetime</w>
-      <w>scale_x_discrete</w>
-      <w>scale_x_log10</w>
-      <w>scale_x_reverse</w>
-      <w>scale_x_sqrt</w>
-      <w>scale_x_time</w>
-      <w>scale_x_yearmon</w>
-      <w>scale_x_yearqtr</w>
-      <w>scale_y_continuous</w>
-      <w>scale_y_date</w>
-      <w>scale_y_datetime</w>
-      <w>scale_y_discrete</w>
-      <w>scale_y_log10</w>
-      <w>scale_y_reverse</w>
-      <w>scale_y_sqrt</w>
-      <w>scale_y_time</w>
-      <w>scale_y_yearmon</w>
-      <w>scale_y_yearqtr</w>
-      <w>scalebar</w>
-      <w>scaledAverage</w>
-      <w>scales</w>
-      <w>scaling</w>
-      <w>scaling.fits</w>
-      <w>scalingFactorTransformation</w>
-      <w>scan</w>
-      <w>scanBam</w>
-      <w>scanBamFlag</w>
-      <w>scanBamHeader</w>
-      <w>scanBamWhat</w>
-      <w>scanBcf</w>
-      <w>scanBcfHeader</w>
-      <w>scanFa</w>
-      <w>scanFaIndex</w>
-      <w>scanPath</w>
-      <w>scanTabix</w>
-      <w>scanVcf</w>
-      <w>scanVcfHeader</w>
-      <w>scanWithPWM</w>
-      <w>scan_stat</w>
-      <w>scans</w>
-      <w>scat</w>
-      <w>scat1d</w>
-      <w>scater</w>
-      <w>scater_gui</w>
-      <w>scatmat</w>
-      <w>scatter.hist</w>
-      <w>scatter.smooth</w>
-      <w>scatter3d</w>
-      <w>scatterHist</w>
-      <w>scatter_plot</w>
-      <w>scatterplot</w>
-      <w>scatterplot3d</w>
-      <w>scatterplotMatrix</w>
-      <w>scb</w>
-      <w>scg</w>
-      <w>scgGrouping</w>
-      <w>scgNormEps</w>
-      <w>scgSemiProjectors</w>
-      <w>scg_eps</w>
-      <w>scg_group</w>
-      <w>scg_semi_proj</w>
-      <w>scheffe</w>
-      <w>schema</w>
-      <w>schemaValidationErrorHandler</w>
-      <w>scheme</w>
-      <w>schiz_genes</w>
-      <w>schmid</w>
-      <w>schweder</w>
-      <w>scientific</w>
-      <w>scientific_format</w>
-      <w>scoped_vars</w>
-      <w>score</w>
-      <w>score.alpha</w>
-      <w>score.binary</w>
-      <w>score.irt</w>
-      <w>score.irt.2</w>
-      <w>score.irt.poly</w>
-      <w>score.items</w>
-      <w>score.multiple.choice</w>
-      <w>scoreFast</w>
-      <w>scoreIrt</w>
-      <w>scoreIrt.1pl</w>
-      <w>scoreIrt.2pl</w>
-      <w>scoreItems</w>
-      <w>scoreOrder</w>
-      <w>scoreOverlap</w>
-      <w>scorePlot</w>
-      <w>scoreShift</w>
-      <w>scoreVeryFast</w>
-      <w>scoreplot</w>
-      <w>scores</w>
-      <w>scoresInTerm</w>
-      <w>scoringMatrix</w>
-      <w>scp</w>
-      <w>scran</w>
-      <w>scree</w>
-      <w>screen</w>
-      <w>screeplot</w>
-      <w>scrub</w>
-      <w>sctransform</w>
-      <w>sd</w>
-      <w>sd.default</w>
-      <w>sd.maxT</w>
-      <w>sd.minP</w>
-      <w>sd2theta</w>
-      <w>sdDiff</w>
-      <w>sdiag</w>
-      <w>se.contrast</w>
-      <w>se.exprs</w>
-      <w>seD</w>
-      <w>seabi</w>
-      <w>seabird</w>
-      <w>seal</w>
-      <w>sealClass</w>
-      <w>sealevel</w>
-      <w>sealevel2</w>
-      <w>seals</w>
-      <w>search</w>
-      <w>searchZeros</w>
-      <w>searchpaths</w>
-      <w>seats</w>
-      <w>sec_axis</w>
-      <w>second</w>
-      <w>seconds</w>
-      <w>seconds_to_period</w>
-      <w>sectionNames</w>
-      <w>sedit</w>
-      <w>seeFastq</w>
-      <w>seeFastqPlot</w>
-      <w>see_if</w>
-      <w>seed</w>
-      <w>seek</w>
-      <w>seek.connection</w>
-      <w>seekViewport</w>
-      <w>seemsS4Object</w>
-      <w>seg.Ar.fit</w>
-      <w>seg.Ar.fit.boot</w>
-      <w>seg.control</w>
-      <w>seg.def.fit</w>
-      <w>seg.def.fit.boot</w>
-      <w>seg.glm.fit</w>
-      <w>seg.glm.fit.boot</w>
-      <w>seg.lm.fit</w>
-      <w>seg.lm.fit.boot</w>
-      <w>seg.sites</w>
-      <w>segment</w>
-      <w>segmentation</w>
-      <w>segmentationData</w>
-      <w>segmented</w>
-      <w>segmented.Arima</w>
-      <w>segmented.default</w>
-      <w>segmented.glm</w>
-      <w>segmented.lm</w>
-      <w>segments</w>
-      <w>segments.p</w>
-      <w>segments.summary</w>
-      <w>segmentsGrob</w>
-      <w>segplot</w>
-      <w>segregmix.init</w>
-      <w>segregmixEM</w>
-      <w>seizure</w>
-      <w>sel2char</w>
-      <w>select</w>
-      <w>select.list</w>
-      <w>select.spatial</w>
-      <w>selectCells</w>
-      <w>selectChannels</w>
-      <w>selectColumns</w>
-      <w>selectDirectory</w>
-      <w>selectEncodingWithCompatibleStrand</w>
-      <w>selectFile</w>
-      <w>selectFromKeys</w>
-      <w>selectHits</w>
-      <w>selectInput</w>
-      <w>selectMethod</w>
-      <w>selectModel</w>
-      <w>selectNcomp</w>
-      <w>selectNearest</w>
-      <w>selectPage</w>
-      <w>selectRows</w>
-      <w>selectSome</w>
-      <w>selectSuperClasses</w>
-      <w>select_</w>
-      <w>select_all</w>
-      <w>select_at</w>
-      <w>select_if</w>
-      <w>select_var</w>
-      <w>select_vars</w>
-      <w>select_vars_</w>
-      <w>selection_factor</w>
-      <w>selectizeInput</w>
-      <w>selectorPlot</w>
-      <w>selfStart</w>
-      <w>selfmatch</w>
-      <w>selfmatchIntegerPairs</w>
-      <w>selfmatchIntegerQuads</w>
-      <w>selm</w>
-      <w>selm.fit</w>
-      <w>sem.diagram</w>
-      <w>sem.graph</w>
-      <w>semat</w>
-      <w>semdata</w>
-      <w>semester</w>
-      <w>semi_join</w>
-      <w>sendCall</w>
-      <w>sendData</w>
-      <w>sendData.MPInode</w>
-      <w>sendData.NWSnode</w>
-      <w>sendData.SOCKnode</w>
-      <w>sendToConsole</w>
-      <w>sendmail</w>
-      <w>sendmailOptions</w>
-      <w>sendmailR</w>
-      <w>sendmail_options</w>
-      <w>sens</w>
-      <w>sensitivity</w>
-      <w>senso</w>
-      <w>sentences</w>
-      <w>sep.bvdata</w>
-      <w>sepUnitsTrans</w>
-      <w>separate</w>
-      <w>separate_</w>
-      <w>separate_rows</w>
-      <w>separate_rows_</w>
-      <w>separates</w>
-      <w>seq</w>
-      <w>seq.Date</w>
-      <w>seq.POSIXt</w>
-      <w>seq.default</w>
-      <w>seq.int</w>
-      <w>seq2gene</w>
-      <w>seq2id</w>
-      <w>seqData</w>
-      <w>seqLogo</w>
-      <w>seqLogoGrid</w>
-      <w>seqToHumanReadable</w>
-      <w>seqToHumanReadable.default</w>
-      <w>seqToIntervals</w>
-      <w>seqToIntervals.default</w>
-      <w>seqXtend</w>
-      <w>seq_along</w>
-      <w>seq_col</w>
-      <w>seq_gradient_pal</w>
-      <w>seq_len</w>
-      <w>seq_mnsl</w>
-      <w>seq_root2tip</w>
-      <w>seq_row</w>
-      <w>seqinfo</w>
-      <w>seqinfo.hg19</w>
-      <w>seqlengths</w>
-      <w>seqlevels</w>
-      <w>seqlevels0</w>
-      <w>seqlevelsInGroup</w>
-      <w>seqlevelsInUse</w>
-      <w>seqlevelsStyle</w>
-      <w>seqnames</w>
-      <w>seqnamesTabix</w>
-      <w>seqtype</w>
-      <w>sequence</w>
-      <w>sequence.lvm</w>
-      <w>sequenceLayer</w>
-      <w>sequenceReport</w>
-      <w>sequential</w>
-      <w>sequential.vertex.coloring</w>
-      <w>sequential_hcl</w>
-      <w>sequential_pal</w>
-      <w>serialize</w>
-      <w>serializeDataPkgEnvs</w>
-      <w>serializeEnv</w>
-      <w>serializeJSON</w>
-      <w>seriate_dendrogram</w>
-      <w>serotonin</w>
-      <w>serotonin2</w>
-      <w>serverInfo</w>
-      <w>service</w>
-      <w>sessionDetails</w>
-      <w>sessionInfo</w>
-      <w>sessionInfoX</w>
-      <w>session_info</w>
-      <w>sessioninfo</w>
-      <w>set</w>
-      <w>set.cor</w>
-      <w>set.edge.attribute</w>
-      <w>set.graph.attribute</w>
-      <w>set.panel</w>
-      <w>set.seed</w>
-      <w>set.vertex.attribute</w>
-      <w>set2key</w>
-      <w>set2keyv</w>
-      <w>setAnnotation</w>
-      <w>setAnnotationHubOption</w>
-      <w>setAs</w>
-      <w>setAttribute</w>
-      <w>setBiocMirror</w>
-      <w>setBitIndicators</w>
-      <w>setBookmarkExclude</w>
-      <w>setBreakpoint</w>
-      <w>setBufLen</w>
-      <w>setCMethod</w>
-      <w>setCRANMirror</w>
-      <w>setChildren</w>
-      <w>setClass</w>
-      <w>setClassUnion</w>
-      <w>setClasses</w>
-      <w>setColNames</w>
-      <w>setColWidths</w>
-      <w>setColors</w>
-      <w>setCompilerOptions</w>
-      <w>setConfig</w>
-      <w>setConstructorS3</w>
-      <w>setConstructorS3.default</w>
-      <w>setCor</w>
-      <w>setCor.diagram</w>
-      <w>setCursorPosition</w>
-      <w>setDF</w>
-      <w>setDT</w>
-      <w>setDTthreads</w>
-      <w>setDataPart</w>
-      <w>setDefaultCluster</w>
-      <w>setDefaultClusterOptions</w>
-      <w>setDefaultLevel</w>
-      <w>setDefaultLevel.Verbose</w>
-      <w>setDoPar</w>
-      <w>setDoSeq</w>
-      <w>setDocumentContents</w>
-      <w>setEPS</w>
-      <w>setESetArgs</w>
-      <w>setExtent</w>
-      <w>setFooter</w>
-      <w>setGeneric</w>
-      <w>setGenericImplicit</w>
-      <w>setGenericS3</w>
-      <w>setGraphicsEventEnv</w>
-      <w>setGraphicsEventHandlers</w>
-      <w>setGrob</w>
-      <w>setGroupGeneric</w>
-      <w>setHDF5DumpCompressionLevel</w>
-      <w>setHDF5DumpDir</w>
-      <w>setHDF5DumpFile</w>
-      <w>setHDF5DumpName</w>
-      <w>setHeader</w>
-      <w>setHeaderFooter</w>
-      <w>setHook</w>
-      <w>setIdentifier</w>
-      <w>setInpBimapFilter</w>
-      <w>setIs</w>
-      <w>setJobFunction</w>
-      <w>setJobNames</w>
-      <w>setLabel</w>
-      <w>setLabel.TextStatusBar</w>
-      <w>setLabels</w>
-      <w>setLabels.TextStatusBar</w>
-      <w>setListElement</w>
-      <w>setLoadAction</w>
-      <w>setLoadActions</w>
-      <w>setMPIcluster</w>
-      <w>setManPath</w>
-      <w>setManPath.Rdoc</w>
-      <w>setMaxValue</w>
-      <w>setMaxValue.ProgressBar</w>
-      <w>setMethod</w>
-      <w>setMethodS3</w>
-      <w>setMethods</w>
-      <w>setMinMax</w>
-      <w>setName</w>
-      <w>setNameFormat</w>
-      <w>setNameFormat.Rdoc</w>
-      <w>setNames</w>
-      <w>setNamespaceInfo</w>
-      <w>setNumericRounding</w>
-      <w>setOldClass</w>
-      <w>setOption</w>
-      <w>setOption.Options</w>
-      <w>setOption.default</w>
-      <w>setPS</w>
-      <w>setPackageExtra</w>
-      <w>setPackageExtraHandler</w>
-      <w>setPackageName</w>
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-      <w>setPackageRegistryEntry</w>
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-      <w>sp2WB</w>
-      <w>sp2tmap</w>
-      <w>spCbind</w>
-      <w>spChFIDs</w>
-      <w>spDists</w>
-      <w>spDistsN1</w>
-      <w>spEM</w>
-      <w>spEMsymloc</w>
-      <w>spEMsymlocN01</w>
-      <w>spLines</w>
-      <w>spMatrix</w>
-      <w>spPolygons</w>
-      <w>spRMM_SEM</w>
-      <w>spRbind</w>
-      <w>spTransform</w>
-      <w>spViewPerFeature</w>
-      <w>space</w>
-      <w>spaghetti</w>
-      <w>spam</w>
-      <w>spam.Version</w>
-      <w>spam.getOption</w>
-      <w>spam.history</w>
-      <w>spam.list</w>
-      <w>spam.numeric</w>
-      <w>spam.options</w>
-      <w>spam.version</w>
-      <w>spam2full</w>
-      <w>spam2spind</w>
-      <w>spam_diag</w>
-      <w>spam_rdist</w>
-      <w>spam_rdist.earth</w>
-      <w>span</w>
-      <w>sparks</w>
-      <w>sparse.model.matrix</w>
-      <w>sparseM2Graph</w>
-      <w>sparseMatrix</w>
-      <w>sparseVector</w>
-      <w>spasm.construct</w>
-      <w>spasm.smooth</w>
-      <w>spasm.sp</w>
-      <w>spatial</w>
-      <w>spatialIndex</w>
-      <w>spatialProcess</w>
-      <w>spatialSign</w>
-      <w>spearman</w>
-      <w>spearman.test</w>
-      <w>spearman2</w>
-      <w>spec</w>
-      <w>spec.ar</w>
-      <w>spec.pgram</w>
-      <w>spec.taper</w>
-      <w>specData</w>
-      <w>spec_csv</w>
-      <w>spec_csv2</w>
-      <w>spec_delim</w>
-      <w>spec_table</w>
-      <w>spec_table2</w>
-      <w>spec_tsv</w>
-      <w>specc</w>
-      <w>speccCBI</w>
-      <w>specgroups</w>
-      <w>species</w>
-      <w>speciesMap</w>
-      <w>speciesTree</w>
-      <w>specificity</w>
-      <w>specify</w>
-      <w>specplot</w>
-      <w>spectra</w>
-      <w>spectrum</w>
-      <w>spectrum0</w>
-      <w>spectrum0.ar</w>
-      <w>spell_check</w>
-      <w>spence.15</w>
-      <w>spence.21</w>
-      <w>spencer</w>
-      <w>sph2cart</w>
-      <w>sphercov</w>
-      <w>spi</w>
-      <w>spi.dictionary</w>
-      <w>spi.keys</w>
-      <w>spider</w>
-      <w>spikeNames</w>
-      <w>spin</w>
-      <w>spin_child</w>
-      <w>spind2full</w>
-      <w>spind2spam</w>
-      <w>spineplot</w>
-      <w>spinglass.community</w>
-      <w>spirals</w>
-      <w>splat</w>
-      <w>splice</w>
-      <w>spliceVariants</w>
-      <w>spline</w>
-      <w>spline.des</w>
-      <w>splineDesign</w>
-      <w>splineKnots</w>
-      <w>splineOrder</w>
-      <w>splinedot</w>
-      <w>splinefun</w>
-      <w>splinefunH</w>
-      <w>splines</w>
-      <w>splint</w>
-      <w>split</w>
-      <w>split.Date</w>
-      <w>split.DelayedArray</w>
-      <w>split.POSIXct</w>
-      <w>split.data.frame</w>
-      <w>split.default</w>
-      <w>split.screen</w>
-      <w>splitAsList</w>
-      <w>splitByCommonTails</w>
-      <w>splitByFacets</w>
-      <w>splitByPattern</w>
-      <w>splitByPattern.default</w>
-      <w>splitCols</w>
-      <w>splitFormula</w>
-      <w>splitFrame</w>
-      <w>splitHalf</w>
-      <w>splitIndices</w>
-      <w>splitIntoGroups</w>
-      <w>splitIntoGroups.DGEList</w>
-      <w>splitIntoGroups.default</w>
-      <w>splitIntoGroupsPseudo</w>
-      <w>splitLayout</w>
-      <w>splitLines4Table</w>
-      <w>splitList</w>
-      <w>splitPath</w>
-      <w>splitRanges</w>
-      <w>splitRegions</w>
-      <w>splitRows</w>
-      <w>splitTime</w>
-      <w>split_indices</w>
-      <w>split_join_distance</w>
-      <w>split_labels</w>
-      <w>split_path</w>
-      <w>split_to_df</w>
-      <w>splitpb</w>
-      <w>splom</w>
-      <w>splsda</w>
-      <w>spm</w>
-      <w>spmap.to.lev</w>
-      <w>spotc</w>
-      <w>spotr</w>
-      <w>spower</w>
-      <w>sppanel</w>
-      <w>spplot</w>
-      <w>spplot.key</w>
-      <w>spplot.locator</w>
-      <w>spread</w>
-      <w>spread.labels</w>
-      <w>spread.level.plot</w>
-      <w>spreadLevelPlot</w>
-      <w>spread_</w>
-      <w>spread_attrs</w>
-      <w>spreadout</w>
-      <w>spregmix</w>
-      <w>sprint</w>
-      <w>sprintf</w>
-      <w>spsample</w>
-      <w>spss.get</w>
-      <w>sql</w>
-      <w>sqlAppendTable</w>
-      <w>sqlAppendTableTemplate</w>
-      <w>sqlColumnToRownames</w>
-      <w>sqlCommentSpec</w>
-      <w>sqlCreateTable</w>
-      <w>sqlData</w>
-      <w>sqlInterpolate</w>
-      <w>sqlParseVariables</w>
-      <w>sqlParseVariablesImpl</w>
-      <w>sqlQuoteSpec</w>
-      <w>sqlRownamesToColumn</w>
-      <w>sql_escape_ident</w>
-      <w>sql_escape_string</w>
-      <w>sql_join</w>
-      <w>sql_select</w>
-      <w>sql_semi_join</w>
-      <w>sql_set_op</w>
-      <w>sql_subquery</w>
-      <w>sql_translate_env</w>
-      <w>sqliteBuildTableDefinition</w>
-      <w>sqliteCopyDatabase</w>
-      <w>sqliteQuickColumn</w>
-      <w>sqrt</w>
-      <w>sqrt_trans</w>
-      <w>sqrtm</w>
-      <w>squarem</w>
-      <w>squeeze</w>
-      <w>squeezeVar</w>
-      <w>squeezedVarOutlierMethod</w>
-      <w>squish</w>
-      <w>squish_infinite</w>
-      <w>srFilter</w>
-      <w>srPhiX174</w>
-      <w>srand</w>
-      <w>src</w>
-      <w>src_df</w>
-      <w>src_local</w>
-      <w>src_mysql</w>
-      <w>src_postgres</w>
-      <w>src_sqlite</w>
-      <w>src_tbls</w>
-      <w>srcfile</w>
-      <w>srcfilealias</w>
-      <w>srcfilecopy</w>
-      <w>srcref</w>
-      <w>srdistance</w>
-      <w>srdistanceFilter</w>
-      <w>srduplicated</w>
-      <w>sread</w>
-      <w>sreg</w>
-      <w>sreg.df.to.lambda</w>
-      <w>sreg.fdf</w>
-      <w>sreg.fgcv</w>
-      <w>sreg.fgcv.model</w>
-      <w>sreg.fgcv.one</w>
-      <w>sreg.fit</w>
-      <w>sreg.fs2hat</w>
-      <w>sreg.trace</w>
-      <w>srisk</w>
-      <w>srlist</w>
-      <w>srorder</w>
-      <w>srrank</w>
-      <w>srsort</w>
-      <w>ss.maxT</w>
-      <w>ss.minP</w>
-      <w>sseg</w>
-      <w>ssh_askpass</w>
-      <w>ssh_path</w>
-      <w>ssl_cert_locations</w>
-      <w>ssn</w>
-      <w>ssva</w>
-      <w>ssvd</w>
-      <w>st.cumulants</w>
-      <w>st.infoMv</w>
-      <w>st.infoUv</w>
-      <w>st.mple</w>
-      <w>stCuts</w>
-      <w>stMincuts</w>
-      <w>st_cuts</w>
-      <w>st_min_cuts</w>
-      <w>stack</w>
-      <w>stackApply</w>
-      <w>stackOpen</w>
-      <w>stackSamples</w>
-      <w>stackSave</w>
-      <w>stackSelect</w>
-      <w>stackStrings</w>
-      <w>stackStringsFromBam</w>
-      <w>stacking</w>
-      <w>stacking_weights</w>
-      <w>stackloss</w>
-      <w>stackpoly</w>
-      <w>stacks</w>
-      <w>stagec</w>
-      <w>stagnant</w>
-      <w>staircase.plot</w>
-      <w>staircasePlot</w>
-      <w>stamp</w>
-      <w>stamp_date</w>
-      <w>stamp_time</w>
-      <w>stan</w>
-      <w>stan_ac</w>
-      <w>stan_demo</w>
-      <w>stan_dens</w>
-      <w>stan_diag</w>
-      <w>stan_ess</w>
-      <w>stan_hist</w>
-      <w>stan_mcse</w>
-      <w>stan_model</w>
-      <w>stan_par</w>
-      <w>stan_plot</w>
-      <w>stan_rdump</w>
-      <w>stan_rhat</w>
-      <w>stan_scat</w>
-      <w>stan_trace</w>
-      <w>stan_version</w>
-      <w>stanc</w>
-      <w>stanc_builder</w>
-      <w>stand_exprs</w>
-      <w>standard.theme</w>
-      <w>standardChromosomes</w>
-      <w>standardGeneric</w>
-      <w>standardise.sumstats.column.headers</w>
-      <w>standardise_aes_names</w>
-      <w>standardise_dep</w>
-      <w>stanford2</w>
-      <w>star</w>
-      <w>starPie</w>
-      <w>stars</w>
-      <w>stars.pval</w>
-      <w>starsCYG</w>
-      <w>start</w>
-      <w>start.dynrq</w>
-      <w>startDaemonizedServer</w>
-      <w>startDynamicHelp</w>
-      <w>startElement.SAX</w>
-      <w>startIndex</w>
-      <w>startPipeServer</w>
-      <w>startServer</w>
-      <w>starter.multigroup</w>
-      <w>startpb</w>
-      <w>startsWith</w>
-      <w>starts_with</w>
-      <w>startupMessage</w>
-      <w>startupMessage.Package</w>
-      <w>startvalues</w>
-      <w>startvalues0</w>
-      <w>startvalues1</w>
-      <w>startvalues2</w>
-      <w>starwars</w>
-      <w>stash</w>
-      <w>stash_apply</w>
-      <w>stash_drop</w>
-      <w>stash_list</w>
-      <w>stash_pop</w>
-      <w>stat</w>
-      <w>stat.anova</w>
-      <w>stat.confband.text</w>
-      <w>stat.gnames</w>
-      <w>stat_bin</w>
-      <w>stat_bin2d</w>
-      <w>stat_bin_2d</w>
-      <w>stat_bin_hex</w>
-      <w>stat_binhex</w>
-      <w>stat_binline</w>
-      <w>stat_boxplot</w>
-      <w>stat_chull</w>
-      <w>stat_compare_means</w>
-      <w>stat_conf_ellipse</w>
-      <w>stat_contour</w>
-      <w>stat_cor</w>
-      <w>stat_count</w>
-      <w>stat_density</w>
-      <w>stat_density2d</w>
-      <w>stat_density_2d</w>
-      <w>stat_density_ridges</w>
-      <w>stat_ecdf</w>
-      <w>stat_ellipse</w>
-      <w>stat_function</w>
-      <w>stat_identity</w>
-      <w>stat_mean</w>
-      <w>stat_plsmo</w>
-      <w>stat_pvalue_manual</w>
-      <w>stat_qq</w>
-      <w>stat_qq_line</w>
-      <w>stat_quantile</w>
-      <w>stat_regline_equation</w>
-      <w>stat_sf</w>
-      <w>stat_sf_coordinates</w>
-      <w>stat_signif</w>
-      <w>stat_smooth</w>
-      <w>stat_spoke</w>
-      <w>stat_stars</w>
-      <w>stat_sum</w>
-      <w>stat_summary</w>
-      <w>stat_summary2d</w>
-      <w>stat_summary_2d</w>
-      <w>stat_summary_bin</w>
-      <w>stat_summary_hex</w>
-      <w>stat_unique</w>
-      <w>stat_ydensity</w>
-      <w>stata.get</w>
-      <w>state.carto.center</w>
-      <w>state.cartoMapEnv</w>
-      <w>state.fips</w>
-      <w>state.vbm</w>
-      <w>state.vbm.center</w>
-      <w>state.vbmMapEnv</w>
-      <w>stateMapEnv</w>
-      <w>statefig</w>
-      <w>statfaculty</w>
-      <w>static.fitness.game</w>
-      <w>static.power.law.game</w>
-      <w>staticClusterApply</w>
-      <w>staticCode</w>
-      <w>staticCode.Object</w>
-      <w>staticPath</w>
-      <w>staticPathOptions</w>
-      <w>stationary.cov</w>
-      <w>stationary.image.cov</w>
-      <w>stationary.taper.cov</w>
-      <w>statmod</w>
-      <w>stats</w>
-      <w>stats.bin</w>
-      <w>stats4</w>
-      <w>statsBy</w>
-      <w>statsBy.boot</w>
-      <w>statsBy.boot.summary</w>
-      <w>status</w>
-      <w>status_code</w>
-      <w>staxlab</w>
-      <w>std.error</w>
-      <w>std.errors</w>
-      <w>stderr</w>
-      <w>stdin</w>
-      <w>stdize</w>
-      <w>stdout</w>
-      <w>stdres</w>
-      <w>steam</w>
-      <w>steamUse</w>
-      <w>stem</w>
-      <w>step</w>
-      <w>stepAIC</w>
-      <w>stepFlexmix</w>
-      <w>step_BoxCox</w>
-      <w>step_YeoJohnson</w>
-      <w>step_arrange</w>
-      <w>step_bagimpute</w>
-      <w>step_bin2factor</w>
-      <w>step_bs</w>
-      <w>step_center</w>
-      <w>step_classdist</w>
-      <w>step_corr</w>
-      <w>step_count</w>
-      <w>step_date</w>
-      <w>step_depth</w>
-      <w>step_discretize</w>
-      <w>step_downsample</w>
-      <w>step_dummy</w>
-      <w>step_factor2string</w>
-      <w>step_filter</w>
-      <w>step_geodist</w>
-      <w>step_holiday</w>
-      <w>step_hyperbolic</w>
-      <w>step_ica</w>
-      <w>step_integer</w>
-      <w>step_interact</w>
-      <w>step_intercept</w>
-      <w>step_inverse</w>
-      <w>step_invlogit</w>
-      <w>step_isomap</w>
-      <w>step_knnimpute</w>
-      <w>step_kpca</w>
-      <w>step_lag</w>
-      <w>step_lincomb</w>
-      <w>step_log</w>
-      <w>step_logit</w>
-      <w>step_lowerimpute</w>
-      <w>step_meanimpute</w>
-      <w>step_medianimpute</w>
-      <w>step_modeimpute</w>
-      <w>step_mutate</w>
-      <w>step_naomit</w>
-      <w>step_nnmf</w>
-      <w>step_novel</w>
-      <w>step_ns</w>
-      <w>step_num2factor</w>
-      <w>step_nzv</w>
-      <w>step_ordinalscore</w>
-      <w>step_other</w>
-      <w>step_pca</w>
-      <w>step_pls</w>
-      <w>step_poly</w>
-      <w>step_profile</w>
-      <w>step_range</w>
-      <w>step_ratio</w>
-      <w>step_regex</w>
-      <w>step_relu</w>
-      <w>step_rm</w>
-      <w>step_rollimpute</w>
-      <w>step_sample</w>
-      <w>step_scale</w>
-      <w>step_shuffle</w>
-      <w>step_slice</w>
-      <w>step_spatialsign</w>
-      <w>step_sqrt</w>
-      <w>step_string2factor</w>
-      <w>step_unorder</w>
-      <w>step_upsample</w>
-      <w>step_window</w>
-      <w>step_zv</w>
-      <w>stepfun</w>
-      <w>stepfun.eval</w>
-      <w>stext</w>
-      <w>stext.default</w>
-      <w>stft</w>
-      <w>still.identical</w>
-      <w>stitch</w>
-      <w>stitch_rhtml</w>
-      <w>stitch_rmd</w>
-      <w>stl</w>
-      <w>stochastic_matrix</w>
-      <w>stogo</w>
-      <w>stop</w>
-      <w>stopAllServers</w>
-      <w>stopApp</w>
-      <w>stopCluster</w>
-      <w>stopCluster.MPIcluster</w>
-      <w>stopCluster.NWScluster</w>
-      <w>stopCluster.default</w>
-      <w>stopCluster.spawnedMPIcluster</w>
-      <w>stopDaemonizedServer</w>
-      <w>stopImplicitCluster</w>
-      <w>stopNode</w>
-      <w>stopServer</w>
-      <w>stopTime</w>
-      <w>stop_for_problems</w>
-      <w>stop_for_status</w>
-      <w>stop_incompatible_cast</w>
-      <w>stop_incompatible_op</w>
-      <w>stop_incompatible_type</w>
-      <w>stopf</w>
-      <w>stopifnot</w>
-      <w>storage.mode</w>
-      <w>storageMode</w>
-      <w>store</w>
-      <w>stormer</w>
-      <w>storms</w>
-      <w>str</w>
-      <w>str.NullVerbose</w>
-      <w>str.Options</w>
-      <w>str.Verbose</w>
-      <w>strOptions</w>
-      <w>strPur1.geneSymbol.LENGTH</w>
-      <w>strPur1.genscan.LENGTH</w>
-      <w>strPur1.refGene.LENGTH</w>
-      <w>strPur1.xenoRefGene.LENGTH</w>
-      <w>strPur2.geneSymbol.LENGTH</w>
-      <w>strPur2.genscan.LENGTH</w>
-      <w>strPur2.refGene.LENGTH</w>
-      <w>strPur2.xenoRefGene.LENGTH</w>
-      <w>str_bs</w>
-      <w>str_c</w>
-      <w>str_class</w>
-      <w>str_conv</w>
-      <w>str_count</w>
-      <w>str_data</w>
-      <w>str_desc</w>
-      <w>str_detect</w>
-      <w>str_diff</w>
-      <w>str_dup</w>
-      <w>str_ends</w>
-      <w>str_extract</w>
-      <w>str_extract_all</w>
-      <w>str_flatten</w>
-      <w>str_fun</w>
-      <w>str_glue</w>
-      <w>str_glue_data</w>
-      <w>str_hash</w>
-      <w>str_interp</w>
-      <w>str_length</w>
-      <w>str_locate</w>
-      <w>str_locate_all</w>
-      <w>str_match</w>
-      <w>str_match_all</w>
-      <w>str_md5sum</w>
-      <w>str_ns</w>
-      <w>str_order</w>
-      <w>str_out</w>
-      <w>str_pad</w>
-      <w>str_pkg</w>
-      <w>str_remove</w>
-      <w>str_remove_all</w>
-      <w>str_replace</w>
-      <w>str_replace_all</w>
-      <w>str_replace_na</w>
-      <w>str_sort</w>
-      <w>str_split</w>
-      <w>str_split_fixed</w>
-      <w>str_squish</w>
-      <w>str_starts</w>
-      <w>str_sub</w>
-      <w>str_subset</w>
-      <w>str_to_lower</w>
-      <w>str_to_sentence</w>
-      <w>str_to_title</w>
-      <w>str_to_upper</w>
-      <w>str_trim</w>
-      <w>str_trunc</w>
-      <w>str_view</w>
-      <w>str_view_all</w>
-      <w>str_which</w>
-      <w>str_wrap</w>
-      <w>strachey</w>
-      <w>strand</w>
-      <w>strandCollapse</w>
-      <w>strandFilter</w>
-      <w>strandMode</w>
-      <w>strandedCounts</w>
-      <w>strata</w>
-      <w>stratify</w>
-      <w>strayDLLs</w>
-      <w>strbreak</w>
-      <w>strcapture</w>
-      <w>strcodes</w>
-      <w>stream_in</w>
-      <w>stream_out</w>
-      <w>stree</w>
-      <w>strength</w>
-      <w>stressvals</w>
-      <w>stretch</w>
-      <w>strftime</w>
-      <w>strgraphwrap</w>
-      <w>strheight</w>
-      <w>stri_c</w>
-      <w>stri_c_list</w>
-      <w>stri_cmp</w>
-      <w>stri_cmp_eq</w>
-      <w>stri_cmp_equiv</w>
-      <w>stri_cmp_ge</w>
-      <w>stri_cmp_gt</w>
-      <w>stri_cmp_le</w>
-      <w>stri_cmp_lt</w>
-      <w>stri_cmp_neq</w>
-      <w>stri_cmp_nequiv</w>
-      <w>stri_compare</w>
-      <w>stri_conv</w>
-      <w>stri_count</w>
-      <w>stri_count_boundaries</w>
-      <w>stri_count_charclass</w>
-      <w>stri_count_coll</w>
-      <w>stri_count_fixed</w>
-      <w>stri_count_regex</w>
-      <w>stri_count_words</w>
-      <w>stri_datetime_add</w>
-      <w>stri_datetime_create</w>
-      <w>stri_datetime_fields</w>
-      <w>stri_datetime_format</w>
-      <w>stri_datetime_fstr</w>
-      <w>stri_datetime_now</w>
-      <w>stri_datetime_parse</w>
-      <w>stri_datetime_symbols</w>
-      <w>stri_detect</w>
-      <w>stri_detect_charclass</w>
-      <w>stri_detect_coll</w>
-      <w>stri_detect_fixed</w>
-      <w>stri_detect_regex</w>
-      <w>stri_dup</w>
-      <w>stri_duplicated</w>
-      <w>stri_duplicated_any</w>
-      <w>stri_enc_detect</w>
-      <w>stri_enc_detect2</w>
-      <w>stri_enc_fromutf32</w>
-      <w>stri_enc_get</w>
-      <w>stri_enc_info</w>
-      <w>stri_enc_isascii</w>
-      <w>stri_enc_isutf16be</w>
-      <w>stri_enc_isutf16le</w>
-      <w>stri_enc_isutf32be</w>
-      <w>stri_enc_isutf32le</w>
-      <w>stri_enc_isutf8</w>
-      <w>stri_enc_list</w>
-      <w>stri_enc_mark</w>
-      <w>stri_enc_set</w>
-      <w>stri_enc_toascii</w>
-      <w>stri_enc_tonative</w>
-      <w>stri_enc_toutf32</w>
-      <w>stri_enc_toutf8</w>
-      <w>stri_encode</w>
-      <w>stri_endswith</w>
-      <w>stri_endswith_charclass</w>
-      <w>stri_endswith_coll</w>
-      <w>stri_endswith_fixed</w>
-      <w>stri_escape_unicode</w>
-      <w>stri_extract</w>
-      <w>stri_extract_all</w>
-      <w>stri_extract_all_boundaries</w>
-      <w>stri_extract_all_charclass</w>
-      <w>stri_extract_all_coll</w>
-      <w>stri_extract_all_fixed</w>
-      <w>stri_extract_all_regex</w>
-      <w>stri_extract_all_words</w>
-      <w>stri_extract_first</w>
-      <w>stri_extract_first_boundaries</w>
-      <w>stri_extract_first_charclass</w>
-      <w>stri_extract_first_coll</w>
-      <w>stri_extract_first_fixed</w>
-      <w>stri_extract_first_regex</w>
-      <w>stri_extract_first_words</w>
-      <w>stri_extract_last</w>
-      <w>stri_extract_last_boundaries</w>
-      <w>stri_extract_last_charclass</w>
-      <w>stri_extract_last_coll</w>
-      <w>stri_extract_last_fixed</w>
-      <w>stri_extract_last_regex</w>
-      <w>stri_extract_last_words</w>
-      <w>stri_flatten</w>
-      <w>stri_info</w>
-      <w>stri_isempty</w>
-      <w>stri_join</w>
-      <w>stri_join_list</w>
-      <w>stri_length</w>
-      <w>stri_list2matrix</w>
-      <w>stri_locale_get</w>
-      <w>stri_locale_info</w>
-      <w>stri_locale_list</w>
-      <w>stri_locale_set</w>
-      <w>stri_locate</w>
-      <w>stri_locate_all</w>
-      <w>stri_locate_all_boundaries</w>
-      <w>stri_locate_all_charclass</w>
-      <w>stri_locate_all_coll</w>
-      <w>stri_locate_all_fixed</w>
-      <w>stri_locate_all_regex</w>
-      <w>stri_locate_all_words</w>
-      <w>stri_locate_first</w>
-      <w>stri_locate_first_boundaries</w>
-      <w>stri_locate_first_charclass</w>
-      <w>stri_locate_first_coll</w>
-      <w>stri_locate_first_fixed</w>
-      <w>stri_locate_first_regex</w>
-      <w>stri_locate_first_words</w>
-      <w>stri_locate_last</w>
-      <w>stri_locate_last_boundaries</w>
-      <w>stri_locate_last_charclass</w>
-      <w>stri_locate_last_coll</w>
-      <w>stri_locate_last_fixed</w>
-      <w>stri_locate_last_regex</w>
-      <w>stri_locate_last_words</w>
-      <w>stri_match</w>
-      <w>stri_match_all</w>
-      <w>stri_match_all_regex</w>
-      <w>stri_match_first</w>
-      <w>stri_match_first_regex</w>
-      <w>stri_match_last</w>
-      <w>stri_match_last_regex</w>
-      <w>stri_na2empty</w>
-      <w>stri_numbytes</w>
-      <w>stri_omit_empty</w>
-      <w>stri_omit_empty_na</w>
-      <w>stri_omit_na</w>
-      <w>stri_opts_brkiter</w>
-      <w>stri_opts_collator</w>
-      <w>stri_opts_fixed</w>
-      <w>stri_opts_regex</w>
-      <w>stri_order</w>
-      <w>stri_pad</w>
-      <w>stri_pad_both</w>
-      <w>stri_pad_left</w>
-      <w>stri_pad_right</w>
-      <w>stri_paste</w>
-      <w>stri_paste_list</w>
-      <w>stri_rand_lipsum</w>
-      <w>stri_rand_shuffle</w>
-      <w>stri_rand_strings</w>
-      <w>stri_read_lines</w>
-      <w>stri_read_raw</w>
-      <w>stri_remove_empty</w>
-      <w>stri_remove_empty_na</w>
-      <w>stri_remove_na</w>
-      <w>stri_replace</w>
-      <w>stri_replace_all</w>
-      <w>stri_replace_all_charclass</w>
-      <w>stri_replace_all_coll</w>
-      <w>stri_replace_all_fixed</w>
-      <w>stri_replace_all_regex</w>
-      <w>stri_replace_first</w>
-      <w>stri_replace_first_charclass</w>
-      <w>stri_replace_first_coll</w>
-      <w>stri_replace_first_fixed</w>
-      <w>stri_replace_first_regex</w>
-      <w>stri_replace_last</w>
-      <w>stri_replace_last_charclass</w>
-      <w>stri_replace_last_coll</w>
-      <w>stri_replace_last_fixed</w>
-      <w>stri_replace_last_regex</w>
-      <w>stri_replace_na</w>
-      <w>stri_reverse</w>
-      <w>stri_sort</w>
-      <w>stri_split</w>
-      <w>stri_split_boundaries</w>
-      <w>stri_split_charclass</w>
-      <w>stri_split_coll</w>
-      <w>stri_split_fixed</w>
-      <w>stri_split_lines</w>
-      <w>stri_split_lines1</w>
-      <w>stri_split_regex</w>
-      <w>stri_startswith</w>
-      <w>stri_startswith_charclass</w>
-      <w>stri_startswith_coll</w>
-      <w>stri_startswith_fixed</w>
-      <w>stri_stats_general</w>
-      <w>stri_stats_latex</w>
-      <w>stri_sub</w>
-      <w>stri_sub_all</w>
-      <w>stri_sub_all_replace</w>
-      <w>stri_sub_replace</w>
-      <w>stri_sub_replace_all</w>
-      <w>stri_subset</w>
-      <w>stri_subset_charclass</w>
-      <w>stri_subset_coll</w>
-      <w>stri_subset_fixed</w>
-      <w>stri_subset_regex</w>
-      <w>stri_timezone_get</w>
-      <w>stri_timezone_info</w>
-      <w>stri_timezone_list</w>
-      <w>stri_timezone_set</w>
-      <w>stri_trans_char</w>
-      <w>stri_trans_general</w>
-      <w>stri_trans_isnfc</w>
-      <w>stri_trans_isnfd</w>
-      <w>stri_trans_isnfkc</w>
-      <w>stri_trans_isnfkc_casefold</w>
-      <w>stri_trans_isnfkd</w>
-      <w>stri_trans_list</w>
-      <w>stri_trans_nfc</w>
-      <w>stri_trans_nfd</w>
-      <w>stri_trans_nfkc</w>
-      <w>stri_trans_nfkc_casefold</w>
-      <w>stri_trans_nfkd</w>
-      <w>stri_trans_tolower</w>
-      <w>stri_trans_totitle</w>
-      <w>stri_trans_toupper</w>
-      <w>stri_trim</w>
-      <w>stri_trim_both</w>
-      <w>stri_trim_left</w>
-      <w>stri_trim_right</w>
-      <w>stri_unescape_unicode</w>
-      <w>stri_unique</w>
-      <w>stri_width</w>
-      <w>stri_wrap</w>
-      <w>stri_write_lines</w>
-      <w>strict_list</w>
-      <w>strikethrough</w>
-      <w>string.bounding.box</w>
-      <w>string.break.line</w>
-      <w>stringAscent</w>
-      <w>stringDescent</w>
-      <w>stringDims</w>
-      <w>stringDist</w>
-      <w>stringHeight</w>
-      <w>stringWidth</w>
-      <w>stringdot</w>
-      <w>stringi</w>
-      <w>stringr</w>
-      <w>stringsAsStrings</w>
-      <w>strings_please</w>
-      <w>strip.custom</w>
-      <w>strip.default</w>
-      <w>strip.terms</w>
-      <w>stripBeadNs</w>
-      <w>stripBeadSDs</w>
-      <w>stripChart</w>
-      <w>stripLabel</w>
-      <w>stripMethyLumiSet</w>
-      <w>stripOOB</w>
-      <w>strip_credentials</w>
-      <w>strip_ctl</w>
-      <w>strip_formula_dots</w>
-      <w>strip_sgr</w>
-      <w>strip_splits</w>
-      <w>strip_style</w>
-      <w>stripchart</w>
-      <w>stripplot</w>
-      <w>strmacro</w>
-      <w>strong</w>
-      <w>strongComp</w>
-      <w>strptime</w>
-      <w>strptimeDate</w>
-      <w>strrep</w>
-      <w>strrepeat</w>
-      <w>strsplit</w>
-      <w>strsplit2</w>
-      <w>strsplitAsListOfIntegerVectors</w>
-      <w>strsplit_ctl</w>
-      <w>strsplit_sgr</w>
-      <w>strtoi</w>
-      <w>strtrim</w>
-      <w>strtrim2_ctl</w>
-      <w>strtrim2_sgr</w>
-      <w>strtrim_ctl</w>
-      <w>strtrim_sgr</w>
-      <w>structure</w>
-      <w>structure.diagram</w>
-      <w>structure.graph</w>
-      <w>structure.list</w>
-      <w>structure.sem</w>
-      <w>strwidth</w>
-      <w>strwrap</w>
-      <w>strwrap2_ctl</w>
-      <w>strwrap2_sgr</w>
-      <w>strwrap_ctl</w>
-      <w>strwrap_sgr</w>
-      <w>student.lvm</w>
-      <w>studres</w>
-      <w>stupidkcentroids</w>
-      <w>stupidknn</w>
-      <w>style</w>
-      <w>styleColorBar</w>
-      <w>styleEqual</w>
-      <w>styleInterval</w>
-      <w>style_blurred</w>
-      <w>style_bold</w>
-      <w>style_dim</w>
-      <w>style_hidden</w>
-      <w>style_inverse</w>
-      <w>style_italic</w>
-      <w>style_na</w>
-      <w>style_neg</w>
-      <w>style_num</w>
-      <w>style_reset</w>
-      <w>style_strikethrough</w>
-      <w>style_subtle</w>
-      <w>style_subtle_num</w>
-      <w>style_underline</w>
-      <w>styles</w>
-      <w>sub</w>
-      <w>subAxt</w>
-      <w>subColSummarizeAvg</w>
-      <w>subColSummarizeAvgLog</w>
-      <w>subColSummarizeBiweight</w>
-      <w>subColSummarizeBiweightLog</w>
-      <w>subColSummarizeLogAvg</w>
-      <w>subColSummarizeLogMedian</w>
-      <w>subColSummarizeMedian</w>
-      <w>subColSummarizeMedianLog</w>
-      <w>subColSummarizeMedianpolish</w>
-      <w>subColSummarizeMedianpolishLog</w>
-      <w>subGraph</w>
-      <w>subListExtract</w>
-      <w>subcomponent</w>
-      <w>subgraph</w>
-      <w>subgraph.centrality</w>
-      <w>subgraph.edges</w>
-      <w>subgraph_centrality</w>
-      <w>subgraph_isomorphic</w>
-      <w>subgraph_isomorphisms</w>
-      <w>subject</w>
-      <w>subjectHits</w>
-      <w>subjectLength</w>
-      <w>submitButton</w>
-      <w>submitJobs</w>
-      <w>submit_cran</w>
-      <w>subnetwork</w>
-      <w>subpatterns</w>
-      <w>subplot</w>
-      <w>subplots</w>
-      <w>subplots.default</w>
-      <w>subrcModelMedianPolish</w>
-      <w>subrcModelPLM</w>
-      <w>subs</w>
-      <w>subseq</w>
-      <w>subset</w>
-      <w>subset.data.frame</w>
-      <w>subset.default</w>
-      <w>subset.matrix</w>
-      <w>subset.spam</w>
-      <w>subsetArgsByFormals</w>
-      <w>subsetByAssay</w>
-      <w>subsetByColData</w>
-      <w>subsetByColumn</w>
-      <w>subsetByFilter</w>
-      <w>subsetByLoci</w>
-      <w>subsetByOverlaps</w>
-      <w>subsetByRow</w>
-      <w>subsetEdgeSets</w>
-      <w>subsetFactors</w>
-      <w>subsetListOfArrays</w>
-      <w>subsetSamples</w>
-      <w>subsetViews</w>
-      <w>subset_seed_as_array</w>
-      <w>subsets</w>
-      <w>substi</w>
-      <w>substi.source</w>
-      <w>substitute</w>
-      <w>substituteDirect</w>
-      <w>substituteFunctionArgs</w>
-      <w>substr</w>
-      <w>substr2_ctl</w>
-      <w>substr2_sgr</w>
-      <w>substr_ctl</w>
-      <w>substr_sgr</w>
-      <w>substring</w>
-      <w>substring.location</w>
-      <w>substring2</w>
-      <w>subsums</w>
-      <w>subtract</w>
-      <w>subtractDependencies</w>
-      <w>subtractRegions</w>
-      <w>subtreeplot</w>
-      <w>subtrees</w>
-      <w>subviews</w>
-      <w>successiveIRanges</w>
-      <w>successiveViews</w>
-      <w>suffix_dataset</w>
-      <w>suffix_extract</w>
-      <w>suffix_refresh</w>
-      <w>suggestAnnotation</w>
-      <w>sum</w>
-      <w>sum.bit</w>
-      <w>sum.bitwhich</w>
-      <w>sum.na</w>
-      <w>sum.ri</w>
-      <w>sum2</w>
-      <w>sumDendrite</w>
-      <w>sumDiss</w>
-      <w>sumOver</w>
-      <w>sumTechReps</w>
-      <w>sumTechReps.DGEList</w>
-      <w>sumTechReps.default</w>
-      <w>sumbrk</w>
-      <w>sumexact</w>
-      <w>sumlog</w>
-      <w>summarise</w>
-      <w>summariseExprsAcrossFeatures</w>
-      <w>summarise_</w>
-      <w>summarise_all</w>
-      <w>summarise_at</w>
-      <w>summarise_coord</w>
-      <w>summarise_each</w>
-      <w>summarise_each_</w>
-      <w>summarise_if</w>
-      <w>summarise_layers</w>
-      <w>summarise_layout</w>
-      <w>summarize</w>
-      <w>summarizeJunctions</w>
-      <w>summarizeOverlaps</w>
-      <w>summarizeRobWeights</w>
-      <w>summarizeToGene</w>
-      <w>summarizeVariants</w>
-      <w>summarize_</w>
-      <w>summarize_CRAN_check_status</w>
-      <w>summarize_all</w>
-      <w>summarize_annotations</w>
-      <w>summarize_at</w>
-      <w>summarize_categorical</w>
-      <w>summarize_check_packages_in_dir_depends</w>
-      <w>summarize_check_packages_in_dir_results</w>
-      <w>summarize_check_packages_in_dir_timings</w>
-      <w>summarize_each</w>
-      <w>summarize_each_</w>
-      <w>summarize_if</w>
-      <w>summarize_numerical</w>
-      <w>summary</w>
-      <w>summary.BootRefFreeEwasModel</w>
-      <w>summary.CA</w>
-      <w>summary.CaGalt</w>
-      <w>summary.DESeqResults</w>
-      <w>summary.Date</w>
-      <w>summary.DiscrFact</w>
-      <w>summary.EList</w>
-      <w>summary.EListRaw</w>
-      <w>summary.FAMD</w>
-      <w>summary.GenomicRanges</w>
-      <w>summary.KRmodcomp</w>
-      <w>summary.Krig</w>
-      <w>summary.MAList</w>
-      <w>summary.MArrayLM</w>
-      <w>summary.MCA</w>
-      <w>summary.MFA</w>
-      <w>summary.Mclust</w>
-      <w>summary.MclustBootstrap</w>
-      <w>summary.MclustDA</w>
-      <w>summary.MclustDR</w>
-      <w>summary.MclustDRsubsel</w>
-      <w>summary.NullVerbose</w>
-      <w>summary.PBmodcomp</w>
-      <w>summary.PCA</w>
-      <w>summary.POSIXct</w>
-      <w>summary.POSIXlt</w>
-      <w>summary.RGList</w>
-      <w>summary.RefFreeCellMix</w>
-      <w>summary.Rle</w>
-      <w>summary.Seqinfo</w>
-      <w>summary.TestResults</w>
-      <w>summary.Verbose</w>
-      <w>summary.aov</w>
-      <w>summary.bagEarth</w>
-      <w>summary.bit</w>
-      <w>summary.bitwhich</w>
-      <w>summary.clustCombi</w>
-      <w>summary.connection</w>
-      <w>summary.cquality</w>
-      <w>summary.crq</w>
-      <w>summary.crqs</w>
-      <w>summary.data.frame</w>
-      <w>summary.default</w>
-      <w>summary.dynrqs</w>
-      <w>summary.factor</w>
-      <w>summary.gam</w>
-      <w>summary.glm</w>
-      <w>summary.gmmhd</w>
-      <w>summary.lars</w>
-      <w>summary.lm</w>
-      <w>summary.mKrig</w>
-      <w>summary.manova</w>
-      <w>summary.matrix</w>
-      <w>summary.mclustBIC</w>
-      <w>summary.mclustICL</w>
-      <w>summary.mergenorm</w>
-      <w>summary.mfpc</w>
-      <w>summary.mixEM</w>
-      <w>summary.mslm</w>
-      <w>summary.mvnpEM</w>
-      <w>summary.ncdf</w>
-      <w>summary.nlrq</w>
-      <w>summary.npEM</w>
-      <w>summary.phylo</w>
-      <w>summary.prabtest</w>
-      <w>summary.proc_time</w>
-      <w>summary.psych</w>
-      <w>summary.qsreg</w>
-      <w>summary.rfpc</w>
-      <w>summary.ri</w>
-      <w>summary.rq</w>
-      <w>summary.rqs</w>
-      <w>summary.rqss</w>
-      <w>summary.segmented</w>
-      <w>summary.sim</w>
-      <w>summary.slm</w>
-      <w>summary.spRMM</w>
-      <w>summary.spam</w>
-      <w>summary.spam.chol.NgPeyton</w>
-      <w>summary.spatialDesign</w>
-      <w>summary.spatialProcess</w>
-      <w>summary.srcfile</w>
-      <w>summary.srcref</w>
-      <w>summary.sreg</w>
-      <w>summary.stepfun</w>
-      <w>summary.table</w>
-      <w>summaryAffyRNAdeg</w>
-      <w>summaryD</w>
-      <w>summaryGCV.Krig</w>
-      <w>summaryGCV.sreg</w>
-      <w>summaryM</w>
-      <w>summaryMclustBIC</w>
-      <w>summaryMclustBICn</w>
-      <w>summaryP</w>
-      <w>summaryRc</w>
-      <w>summaryRprof</w>
-      <w>summaryS</w>
-      <w>summitOverlaps</w>
-      <w>summits</w>
-      <w>sump</w>
-      <w>sumstatsColHeaders</w>
-      <w>sumt</w>
-      <w>sumz</w>
-      <w>sunflowerplot</w>
-      <w>sunriset</w>
-      <w>sunspot.month</w>
-      <w>sunspot.year</w>
-      <w>sunspots</w>
-      <w>super.matrix</w>
-      <w>superClassDepth</w>
-      <w>superMatrix</w>
-      <w>supportedFilters</w>
-      <w>supportedGeneIDs</w>
-      <w>supportedGenomes</w>
-      <w>supportedMiRBaseBuildValues</w>
-      <w>supportedOrganisms</w>
-      <w>supportedRealizationBackends</w>
-      <w>supportedSeqlevelsStyles</w>
-      <w>supportedUCSCFeatureDbTables</w>
-      <w>supportedUCSCFeatureDbTracks</w>
-      <w>supportedUCSCtables</w>
-      <w>supportsArg</w>
-      <w>supportsExpat</w>
-      <w>supportsLibxml</w>
-      <w>supportsMulticore</w>
-      <w>suppressAll</w>
-      <w>suppressDependencies</w>
-      <w>suppressForeignCheck</w>
-      <w>suppressMessages</w>
-      <w>suppressPackageStartupMessages</w>
-      <w>suppressWarnings</w>
-      <w>supsmu</w>
-      <w>surf.gls</w>
-      <w>surf.ls</w>
-      <w>surf.tri</w>
-      <w>surface</w>
-      <w>surface.Krig</w>
-      <w>surface.default</w>
-      <w>surface.mKrig</w>
-      <w>surfaceArea</w>
-      <w>surfacePlot</w>
-      <w>surroundSingletons</w>
-      <w>survConcordance</w>
-      <w>survConcordance.fit</w>
-      <w>survModel</w>
-      <w>survReg</w>
-      <w>survSplit</w>
-      <w>survdiff</w>
-      <w>survexp</w>
-      <w>survey</w>
-      <w>survfit</w>
-      <w>survfit.formula</w>
-      <w>survfitCI</w>
-      <w>survfitKM</w>
-      <w>survfitcoxph.fit</w>
-      <w>survival</w>
-      <w>survobrien</w>
-      <w>survpenal.fit</w>
-      <w>survreg</w>
-      <w>survreg.control</w>
-      <w>survreg.distributions</w>
-      <w>survreg.fit</w>
-      <w>survregDtest</w>
-      <w>survuh</w>
-      <w>sva</w>
-      <w>sva.check</w>
-      <w>svaseq</w>
-      <w>svd</w>
-      <w>svd.triplet</w>
-      <w>svdSafe</w>
-      <w>svdpc.fit</w>
-      <w>svdr</w>
-      <w>svg</w>
-      <w>svm</w>
-      <w>svmBag</w>
-      <w>svn.time</w>
-      <w>swan</w>
-      <w>swap</w>
-      <w>swapXY</w>
-      <w>swapXY.density</w>
-      <w>swarmx</w>
-      <w>swarmy</w>
-      <w>swatchplot</w>
-      <w>sweep</w>
-      <w>sweepRegistry</w>
-      <w>swirl</w>
-      <w>swiss</w>
-      <w>swiss_prot</w>
-      <w>swissbank</w>
-      <w>switch</w>
-      <w>swlm</w>
-      <w>sylvester</w>
-      <w>sym</w>
-      <w>symCount</w>
-      <w>symLink2bam</w>
-      <w>symbol</w>
-      <w>symbol.freq</w>
-      <w>symbolToR</w>
-      <w>symbolbarplot</w>
-      <w>symbolbox</w>
-      <w>symbolize</w>
-      <w>symbols</w>
-      <w>symbolsGrob</w>
-      <w>symbolsInPolys</w>
-      <w>symbox</w>
-      <w>symdif</w>
-      <w>symdiff</w>
-      <w>symmetric1</w>
-      <w>symmetric2</w>
-      <w>symmetricP0</w>
-      <w>symmetricP05</w>
-      <w>symmetricP1</w>
-      <w>symmetricP2</w>
-      <w>symmpart</w>
-      <w>symnum</w>
-      <w>syms</w>
-      <w>syncRegistry</w>
-      <w>syntenicDotplot</w>
-      <w>synth.te</w>
-      <w>synth.tr</w>
-      <w>sys</w>
-      <w>sys.call</w>
-      <w>sys.calls</w>
-      <w>sys.frame</w>
-      <w>sys.frames</w>
-      <w>sys.function</w>
-      <w>sys.load.image</w>
-      <w>sys.nframe</w>
-      <w>sys.on.exit</w>
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-      <w>sys.save.image</w>
-      <w>sys.source</w>
-      <w>sys.status</w>
-      <w>sysargs</w>
-      <w>system</w>
-      <w>system.file</w>
-      <w>system.time</w>
-      <w>system2</w>
-      <w>system3</w>
-      <w>systemArgs</w>
-      <w>systemPipeR</w>
-      <w>systemR</w>
-      <w>systemR.default</w>
-      <w>system_check</w>
-      <w>system_output</w>
-      <w>systematicSubset</w>
-      <w>t</w>
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-      <w>t.HitsList</w>
-      <w>t.data.frame</w>
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-      <w>t2</w>
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-      <w>t2r</w>
-      <w>tQuantTrans</w>
-      <w>tRNAs</w>
-      <w>tSNE</w>
-      <w>tZscore</w>
-      <w>t_tx_OP_y</w>
-      <w>tab.disjonctif</w>
-      <w>tab.disjonctif.prop</w>
-      <w>tab.title</w>
-      <w>tabBox</w>
-      <w>tabItem</w>
-      <w>tabItems</w>
-      <w>tabPanel</w>
-      <w>table</w>
-      <w>table.rq</w>
-      <w>table1</w>
-      <w>table2</w>
-      <w>table2df</w>
-      <w>table2html</w>
-      <w>table2matrix</w>
-      <w>table3</w>
-      <w>table4a</w>
-      <w>table4b</w>
-      <w>table5</w>
-      <w>tableF</w>
-      <w>tableFooter</w>
-      <w>tableGrob</w>
-      <w>tableHeader</w>
-      <w>tableName</w>
-      <w>tableNames</w>
-      <w>tableOutput</w>
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-      <w>table_cell_bg</w>
-      <w>table_cell_font</w>
-      <w>table_formatpct</w>
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-      <w>table_latexdefs</w>
-      <w>table_pc</w>
-      <w>table_trio</w>
-      <w>tables</w>
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-      <w>tabsetPanel</w>
-      <w>tabulate</w>
-      <w>tabulr</w>
-      <w>tae</w>
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-      <w>taeGut1.geneSymbol.LENGTH</w>
-      <w>taeGut1.genscan.LENGTH</w>
-      <w>taeGut1.nscanGene.LENGTH</w>
-      <w>taeGut1.refGene.LENGTH</w>
-      <w>taeGut1.xenoRefGene.LENGTH</w>
-      <w>tag</w>
-      <w>tagAppendAttributes</w>
-      <w>tagAppendChild</w>
-      <w>tagAppendChildren</w>
-      <w>tagClusters</w>
-      <w>tagGetAttribute</w>
-      <w>tagHasAttribute</w>
-      <w>tagHeatmap</w>
-      <w>tagList</w>
-      <w>tagMatrixList</w>
-      <w>tagSetChildren</w>
-      <w>tag_delete</w>
-      <w>tagged_na</w>
-      <w>tagname</w>
-      <w>tags</w>
-      <w>tai</w>
-      <w>tail</w>
-      <w>tail.DataTable</w>
-      <w>tail.LLint</w>
-      <w>tail.Vector</w>
-      <w>tail.matrix</w>
-      <w>tail.spam</w>
-      <w>tail_of</w>
-      <w>tail_while</w>
-      <w>take</w>
-      <w>takeSingletons</w>
-      <w>tally</w>
-      <w>tally_</w>
-      <w>tan</w>
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-      <w>tanh</w>
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-      <w>tanpi</w>
-      <w>tapply</w>
-      <w>tapplySimpl</w>
-      <w>tar</w>
-      <w>target.rot</w>
-      <w>targetID2nuID</w>
-      <w>targetRanges</w>
-      <w>targetSeqs</w>
-      <w>targetedGenes</w>
-      <w>targets</w>
-      <w>targetsA2C</w>
-      <w>targetsheader</w>
-      <w>targetsin</w>
-      <w>targetsout</w>
-      <w>taskCallbackManager</w>
-      <w>taskItem</w>
-      <w>tau</w>
-      <w>tau.nlrq</w>
-      <w>tauequivnormalmixEM</w>
-      <w>taxonomyId</w>
-      <w>taylor.diagram</w>
-      <w>tb</w>
-      <w>tb.width</w>
-      <w>tbl</w>
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-      <w>tblNoNext</w>
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-      <w>tbl_sum</w>
-      <w>tbl_vars</w>
-      <w>tbody_style</w>
-      <w>tcgaPipeline</w>
-      <w>tcl</w>
-      <w>tclArray</w>
-      <w>tclObj</w>
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-      <w>tclclose</w>
-      <w>tclfile.dir</w>
-      <w>tclfile.tail</w>
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-      <w>tclustCBI</w>
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-      <w>tclvar</w>
-      <w>tcoffee</w>
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-      <w>tcrossapply_simple_triplet_matrix</w>
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-      <w>tcrossprod_simple_triplet_matrix</w>
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-      <w>telef</w>
-      <w>tempdir</w>
-      <w>temper</w>
-      <w>tempfile</w>
-      <w>tempvar</w>
-      <w>tenberge</w>
-      <w>tennis_MvsF</w>
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-      <w>termGraphs</w>
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-      <w>terminalCreate</w>
-      <w>terminalExecute</w>
-      <w>terminalExitCode</w>
-      <w>terminalKill</w>
-      <w>terminalList</w>
-      <w>terminalRunning</w>
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-      <w>terminalVisible</w>
-      <w>termplot</w>
-      <w>terms</w>
-      <w>terms.formula</w>
-      <w>termsDrop</w>
-      <w>terms_select</w>
-      <w>terrain</w>
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-      <w>terrain_hcl</w>
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-      <w>test.psych</w>
-      <w>testBioCConnection</w>
-      <w>testDF</w>
-      <w>testDataSet</w>
-      <w>testDateTime</w>
-      <w>testDirection</w>
-      <w>testForValidKeytype</w>
-      <w>testInheritedMethods</w>
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-      <w>testName</w>
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-      <w>testPerl</w>
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-      <w>testRversion</w>
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-      <w>testStatPar</w>
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-      <w>testTransform</w>
-      <w>testVar</w>
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-      <w>test_coverage_file</w>
-      <w>test_file</w>
-      <w>testnslv</w>
-      <w>testpanelGroupBreak</w>
-      <w>testpanelSubjectBreak</w>
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-      <w>tetNig2.ensGene.LENGTH</w>
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-      <w>tetragonula</w>
-      <w>tetramesh</w>
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-      <w>texi2pdf</w>
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-      <w>text.default</w>
-      <w>textAreaInput</w>
-      <w>textConnection</w>
-      <w>textConnectionValue</w>
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-      <w>textInput</w>
-      <w>textOutput</w>
-      <w>text_colour</w>
-      <w>text_content</w>
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-      <w>textbox</w>
-      <w>textplot</w>
-      <w>textual</w>
-      <w>thayer</w>
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-      <w>theEconomist.opts</w>
-      <w>theEconomist.theme</w>
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-      <w>theme_bw</w>
-      <w>theme_classic</w>
-      <w>theme_classic2</w>
-      <w>theme_cleveland</w>
-      <w>theme_cowplot</w>
-      <w>theme_dark</w>
-      <w>theme_dendro</w>
-      <w>theme_dose</w>
-      <w>theme_get</w>
-      <w>theme_gray</w>
-      <w>theme_grey</w>
-      <w>theme_light</w>
-      <w>theme_linedraw</w>
-      <w>theme_map</w>
-      <w>theme_minimal</w>
-      <w>theme_nothing</w>
-      <w>theme_pubclean</w>
-      <w>theme_pubr</w>
-      <w>theme_replace</w>
-      <w>theme_ridges</w>
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-      <w>theme_test</w>
-      <w>theme_transparent</w>
-      <w>theme_update</w>
-      <w>theme_void</w>
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-      <w>threeUTRsByTranscript</w>
-      <w>threebands</w>
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-      <w>thresholder</w>
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-      <w>throw</w>
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-      <w>tibble_</w>
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-      <w>tidy_eval</w>
-      <w>tidy_file</w>
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-      <w>tidy_label_colours</w>
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-      <w>tiff</w>
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-      <w>timeLastDayInQuarter</w>
-      <w>timeLastNdayInMonth</w>
-      <w>timeNdayOnOrAfter</w>
-      <w>timeNdayOnOrBefore</w>
-      <w>timeNthNdayInMonth</w>
-      <w>timeSequence</w>
-      <w>time_ago</w>
-      <w>time_bins</w>
-      <w>time_format</w>
-      <w>time_length</w>
-      <w>time_trans</w>
-      <w>timedep</w>
-      <w>timeout</w>
-      <w>timepoints</w>
-      <w>timerProgressBar</w>
-      <w>times</w>
-      <w>timestamp</w>
-      <w>timestamp.Verbose</w>
-      <w>timestamp.default</w>
-      <w>timestampOff</w>
-      <w>timestampOff.Verbose</w>
-      <w>timestampOn</w>
-      <w>timestampOn.Verbose</w>
-      <w>timetaken</w>
-      <w>tinytex</w>
-      <w>tinytex_root</w>
-      <w>tiplabels</w>
-      <w>tips</w>
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-      <w>tips_MvsF</w>
-      <w>title</w>
-      <w>titlePanel</w>
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-      <w>tkStartGUI</w>
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-      <w>tkXselection.handle</w>
-      <w>tkXselection.own</w>
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-      <w>tk_choose.dir</w>
-      <w>tk_choose.files</w>
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-      <w>tk_coords</w>
-      <w>tk_fit</w>
-      <w>tk_messageBox</w>
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-      <w>tk_postscript</w>
-      <w>tk_reshape</w>
-      <w>tk_rotate</w>
-      <w>tk_select.list</w>
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-      <w>tkcget</w>
-      <w>tkcheckbutton</w>
-      <w>tkchooseDirectory</w>
-      <w>tkclipboard.append</w>
-      <w>tkclipboard.clear</w>
-      <w>tkcompare</w>
-      <w>tkconfigure</w>
-      <w>tkcoords</w>
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-      <w>tkcurselection</w>
-      <w>tkdchars</w>
-      <w>tkdebug</w>
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-      <w>tkdensity</w>
-      <w>tkdeselect</w>
-      <w>tkdestroy</w>
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-      <w>tkdlineinfo</w>
-      <w>tkdtag</w>
-      <w>tkdump</w>
-      <w>tkentry</w>
-      <w>tkentrycget</w>
-      <w>tkentryconfigure</w>
-      <w>tkevent.add</w>
-      <w>tkevent.delete</w>
-      <w>tkevent.generate</w>
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-      <w>tkfind</w>
-      <w>tkflash</w>
-      <w>tkfocus</w>
-      <w>tkfont.actual</w>
-      <w>tkfont.configure</w>
-      <w>tkfont.create</w>
-      <w>tkfont.delete</w>
-      <w>tkfont.families</w>
-      <w>tkfont.measure</w>
-      <w>tkfont.metrics</w>
-      <w>tkfont.names</w>
-      <w>tkfraction</w>
-      <w>tkframe</w>
-      <w>tkget</w>
-      <w>tkgetOpenFile</w>
-      <w>tkgetSaveFile</w>
-      <w>tkgettags</w>
-      <w>tkgrab</w>
-      <w>tkgrab.current</w>
-      <w>tkgrab.release</w>
-      <w>tkgrab.set</w>
-      <w>tkgrab.status</w>
-      <w>tkgrid</w>
-      <w>tkgrid.bbox</w>
-      <w>tkgrid.columnconfigure</w>
-      <w>tkgrid.configure</w>
-      <w>tkgrid.forget</w>
-      <w>tkgrid.info</w>
-      <w>tkgrid.location</w>
-      <w>tkgrid.propagate</w>
-      <w>tkgrid.remove</w>
-      <w>tkgrid.rowconfigure</w>
-      <w>tkgrid.size</w>
-      <w>tkgrid.slaves</w>
-      <w>tkicursor</w>
-      <w>tkidentify</w>
-      <w>tkigraph</w>
-      <w>tkimage.create</w>
-      <w>tkimage.delete</w>
-      <w>tkimage.height</w>
-      <w>tkimage.inuse</w>
-      <w>tkimage.names</w>
-      <w>tkimage.type</w>
-      <w>tkimage.types</w>
-      <w>tkimage.width</w>
-      <w>tkindex</w>
-      <w>tkinsert</w>
-      <w>tkinvoke</w>
-      <w>tkitembind</w>
-      <w>tkitemcget</w>
-      <w>tkitemconfigure</w>
-      <w>tkitemfocus</w>
-      <w>tkitemlower</w>
-      <w>tkitemraise</w>
-      <w>tkitemscale</w>
-      <w>tklabel</w>
-      <w>tklistbox</w>
-      <w>tklower</w>
-      <w>tkmark.gravity</w>
-      <w>tkmark.names</w>
-      <w>tkmark.next</w>
-      <w>tkmark.previous</w>
-      <w>tkmark.set</w>
-      <w>tkmark.unset</w>
-      <w>tkmeans</w>
-      <w>tkmenu</w>
-      <w>tkmenubutton</w>
-      <w>tkmessage</w>
-      <w>tkmessageBox</w>
-      <w>tkmove</w>
-      <w>tknearest</w>
-      <w>tkpack</w>
-      <w>tkpack.configure</w>
-      <w>tkpack.forget</w>
-      <w>tkpack.info</w>
-      <w>tkpack.propagate</w>
-      <w>tkpack.slaves</w>
-      <w>tkpager</w>
-      <w>tkplace</w>
-      <w>tkplace.configure</w>
-      <w>tkplace.forget</w>
-      <w>tkplace.info</w>
-      <w>tkplace.slaves</w>
-      <w>tkplot</w>
-      <w>tkplot.canvas</w>
-      <w>tkplot.center</w>
-      <w>tkplot.close</w>
-      <w>tkplot.export.postscript</w>
-      <w>tkplot.fit.to.screen</w>
-      <w>tkplot.getcoords</w>
-      <w>tkplot.off</w>
-      <w>tkplot.reshape</w>
-      <w>tkplot.rotate</w>
-      <w>tkplot.setcoords</w>
-      <w>tkpopup</w>
-      <w>tkpost</w>
-      <w>tkpostcascade</w>
-      <w>tkpostscript</w>
-      <w>tkradiobutton</w>
-      <w>tkraise</w>
-      <w>tkscale</w>
-      <w>tkscan.dragto</w>
-      <w>tkscan.mark</w>
-      <w>tkscrollbar</w>
-      <w>tksearch</w>
-      <w>tksee</w>
-      <w>tkselect</w>
-      <w>tkselection.adjust</w>
-      <w>tkselection.anchor</w>
-      <w>tkselection.clear</w>
-      <w>tkselection.from</w>
-      <w>tkselection.includes</w>
-      <w>tkselection.present</w>
-      <w>tkselection.range</w>
-      <w>tkselection.set</w>
-      <w>tkselection.to</w>
-      <w>tkset</w>
-      <w>tksize</w>
-      <w>tktag.add</w>
-      <w>tktag.bind</w>
-      <w>tktag.cget</w>
-      <w>tktag.configure</w>
-      <w>tktag.delete</w>
-      <w>tktag.lower</w>
-      <w>tktag.names</w>
-      <w>tktag.nextrange</w>
-      <w>tktag.prevrange</w>
-      <w>tktag.raise</w>
-      <w>tktag.ranges</w>
-      <w>tktag.remove</w>
-      <w>tktext</w>
-      <w>tktitle</w>
-      <w>tktoggle</w>
-      <w>tktoplevel</w>
-      <w>tktype</w>
-      <w>tkunpost</w>
-      <w>tkwait.variable</w>
-      <w>tkwait.visibility</w>
-      <w>tkwait.window</w>
-      <w>tkwidget</w>
-      <w>tkwindow.cget</w>
-      <w>tkwindow.configure</w>
-      <w>tkwindow.create</w>
-      <w>tkwindow.names</w>
-      <w>tkwinfo</w>
-      <w>tkwm.aspect</w>
-      <w>tkwm.client</w>
-      <w>tkwm.colormapwindows</w>
-      <w>tkwm.command</w>
-      <w>tkwm.deiconify</w>
-      <w>tkwm.focusmodel</w>
-      <w>tkwm.frame</w>
-      <w>tkwm.geometry</w>
-      <w>tkwm.grid</w>
-      <w>tkwm.group</w>
-      <w>tkwm.iconbitmap</w>
-      <w>tkwm.iconify</w>
-      <w>tkwm.iconmask</w>
-      <w>tkwm.iconname</w>
-      <w>tkwm.iconposition</w>
-      <w>tkwm.iconwindow</w>
-      <w>tkwm.maxsize</w>
-      <w>tkwm.minsize</w>
-      <w>tkwm.overrideredirect</w>
-      <w>tkwm.positionfrom</w>
-      <w>tkwm.protocol</w>
-      <w>tkwm.resizable</w>
-      <w>tkwm.sizefrom</w>
-      <w>tkwm.state</w>
-      <w>tkwm.title</w>
-      <w>tkwm.transient</w>
-      <w>tkwm.withdraw</w>
-      <w>tkxview</w>
-      <w>tkxview.moveto</w>
-      <w>tkxview.scroll</w>
-      <w>tkyposition</w>
-      <w>tkyview</w>
-      <w>tkyview.moveto</w>
-      <w>tkyview.scroll</w>
-      <w>tl_pkgs</w>
-      <w>tl_sizes</w>
-      <w>tld_dataset</w>
-      <w>tld_extract</w>
-      <w>tld_refresh</w>
-      <w>tli</w>
-      <w>tlmgr</w>
-      <w>tlmgr_conf</w>
-      <w>tlmgr_install</w>
-      <w>tlmgr_path</w>
-      <w>tlmgr_remove</w>
-      <w>tlmgr_search</w>
-      <w>tlmgr_update</w>
-      <w>tmd</w>
-      <w>tmerge</w>
-      <w>tmixture.matrix</w>
-      <w>tmixture.vector</w>
-      <w>tmpDir</w>
-      <w>tmpfile</w>
-      <w>tnewton</w>
-      <w>tnr</w>
-      <w>to</w>
-      <w>to.mesh3d</w>
-      <w>toAsciiRegExprPattern</w>
-      <w>toAsciiRegExprPattern.character</w>
-      <w>toBibtex</w>
-      <w>toBroadXML</w>
-      <w>toCamelCase</w>
-      <w>toCamelCase.default</w>
-      <w>toCellDataSet</w>
-      <w>toComplex</w>
-      <w>toDataframe</w>
-      <w>toDot</w>
-      <w>toDotR</w>
-      <w>toDotWithRI</w>
-      <w>toFile</w>
-      <w>toFileListTree</w>
-      <w>toFileListTree.character</w>
-      <w>toGRanges</w>
-      <w>toGXL</w>
-      <w>toGmt</w>
-      <w>toHTML</w>
-      <w>toJSON</w>
-      <w>toLatex</w>
-      <w>toLatex.xtable</w>
-      <w>toPWM</w>
-      <w>toRGB</w>
-      <w>toRangeStr</w>
-      <w>toRd</w>
-      <w>toSAF</w>
-      <w>toSQLStringSet</w>
-      <w>toSingleCellExperiment</w>
-      <w>toString</w>
-      <w>toString.XMLNode</w>
-      <w>toString.default</w>
-      <w>toTable</w>
-      <w>toTitleCase</w>
-      <w>toUrl</w>
-      <w>toUrl.default</w>
-      <w>toWebGL</w>
-      <w>to_basic</w>
-      <w>to_string</w>
-      <w>to_string_v</w>
-      <w>tobase64image</w>
-      <w>tobin</w>
-      <w>today</w>
-      <w>todo</w>
-      <w>toeplitz</w>
-      <w>toeplitz.spam</w>
-      <w>toformula</w>
-      <w>toggle</w>
-      <w>toggleClass</w>
-      <w>toggleCssClass</w>
-      <w>toggleElement</w>
-      <w>toggleProbes</w>
-      <w>toggleState</w>
-      <w>togglefun</w>
-      <w>togglep</w>
-      <w>togglez</w>
-      <w>togroup</w>
-      <w>togrouplength</w>
-      <w>togrouprank</w>
-      <w>tojson</w>
-      <w>tojulian</w>
-      <w>tokenize</w>
-      <w>tokenize_file</w>
-      <w>tokenize_string</w>
-      <w>tokenizer_csv</w>
-      <w>tokenizer_delim</w>
-      <w>tokenizer_fwf</w>
-      <w>tokenizer_line</w>
-      <w>tokenizer_log</w>
-      <w>tokenizer_tsv</w>
-      <w>tokenizer_ws</w>
-      <w>tolEllipsePlot</w>
-      <w>tolerance</w>
-      <w>tolower</w>
-      <w>tomogplot</w>
-      <w>tonedata</w>
-      <w>tools</w>
-      <w>topBottom</w>
-      <w>topBottomDistribute</w>
-      <w>topGO</w>
-      <w>topGSA</w>
-      <w>topKEGG</w>
-      <w>topPage</w>
-      <w>topRUV</w>
-      <w>topRomer</w>
-      <w>topSplice</w>
-      <w>topSpliceDGE</w>
-      <w>topTable</w>
-      <w>topTableF</w>
-      <w>topTags</w>
-      <w>topTreat</w>
-      <w>topVar</w>
-      <w>top_n</w>
-      <w>topedges</w>
-      <w>topenv</w>
-      <w>topmodels</w>
-      <w>topns</w>
-      <w>topns_name</w>
-      <w>topo</w>
-      <w>topo.colors</w>
-      <w>topo_sort</w>
-      <w>topological.sort</w>
-      <w>toprab</w>
-      <w>toptable</w>
-      <w>tost</w>
-      <w>total.intensity</w>
-      <w>totalDepth</w>
-      <w>totalPenaltySpace</w>
-      <w>total_correlation</w>
-      <w>totaleffects</w>
-      <w>touchFile</w>
-      <w>touchFile.default</w>
-      <w>toupper</w>
-      <w>toxicity</w>
-      <w>toxocara</w>
-      <w>tpm</w>
-      <w>tpr</w>
-      <w>tr</w>
-      <w>trace</w>
-      <w>traceOff</w>
-      <w>traceOn</w>
-      <w>traceback</w>
-      <w>tracemem</w>
-      <w>traceplot</w>
-      <w>tracingState</w>
-      <w>track</w>
-      <w>trackAzimuth</w>
-      <w>trackList</w>
-      <w>trackName</w>
-      <w>trackNames</w>
-      <w>trackViewer</w>
-      <w>trackViewerStyle</w>
-      <w>tracker</w>
-      <w>trafo</w>
-      <w>train</w>
-      <w>trainControl</w>
-      <w>trainCurveELBO</w>
-      <w>trainCurveFactors</w>
-      <w>train_continuous</w>
-      <w>train_discrete</w>
-      <w>traits</w>
-      <w>traits_callaway</w>
-      <w>trans</w>
-      <w>trans3d</w>
-      <w>trans_breaks</w>
-      <w>trans_format</w>
-      <w>trans_new</w>
-      <w>trans_range</w>
-      <w>transace</w>
-      <w>transcan</w>
-      <w>transcript</w>
-      <w>transcriptLengths</w>
-      <w>transcriptLocs2refLocs</w>
-      <w>transcriptWidths</w>
-      <w>transcripts</w>
-      <w>transcriptsBy</w>
-      <w>transcriptsByOverlaps</w>
-      <w>transf</w>
-      <w>transform</w>
-      <w>transform.data.frame</w>
-      <w>transform.default</w>
-      <w>transformDfToGr</w>
-      <w>transformGRangesForEvenSpace</w>
-      <w>transformToBarInCircle</w>
-      <w>transformToCircle</w>
-      <w>transformToDf</w>
-      <w>transformToGenome</w>
-      <w>transformToLinkInCircle</w>
-      <w>transformToRectInCircle</w>
-      <w>transformToSegInCircle</w>
-      <w>transform_position</w>
-      <w>transformx</w>
-      <w>transitive.closure</w>
-      <w>transitivity</w>
-      <w>translate</w>
-      <w>translateLocalUrl</w>
-      <w>transmute</w>
-      <w>transmute_</w>
-      <w>transmute_all</w>
-      <w>transmute_at</w>
-      <w>transmute_if</w>
-      <w>transparent</w>
-      <w>transplant</w>
-      <w>transpose</w>
-      <w>trap.rule</w>
-      <w>trapezint</w>
-      <w>trapz</w>
-      <w>treat</w>
-      <w>tree</w>
-      <w>treeInfo</w>
-      <w>treeLevels</w>
-      <w>treePop</w>
-      <w>treebagFuncs</w>
-      <w>treebagGA</w>
-      <w>treebagSA</w>
-      <w>treebagSBF</w>
-      <w>treering</w>
-      <w>trees</w>
-      <w>trellis.currentLayout</w>
-      <w>trellis.device</w>
-      <w>trellis.focus</w>
-      <w>trellis.grobname</w>
-      <w>trellis.last.object</w>
-      <w>trellis.panelArgs</w>
-      <w>trellis.par.get</w>
-      <w>trellis.par.set</w>
-      <w>trellis.strip.blank</w>
-      <w>trellis.switchFocus</w>
-      <w>trellis.unfocus</w>
-      <w>trellis.vpname</w>
-      <w>trend.ebam</w>
-      <w>trend.stat</w>
-      <w>trendVar</w>
-      <w>trex</w>
-      <w>tri.ineq.show</w>
-      <w>triad.census</w>
-      <w>triadCensus</w>
-      <w>triad_census</w>
-      <w>triangMtd</w>
-      <w>triangMtds</w>
-      <w>triangleFixing</w>
-      <w>triangles</w>
-      <w>triax.abline</w>
-      <w>triax.fill</w>
-      <w>triax.frame</w>
-      <w>triax.plot</w>
-      <w>triax.points</w>
-      <w>tribble</w>
-      <w>tribolium</w>
-      <w>trichol</w>
-      <w>tricubeMovingAverage</w>
-      <w>trie</w>
-      <w>trie_add</w>
-      <w>trie_remove</w>
-      <w>triebeard</w>
-      <w>trigamma</w>
-      <w>trigammaInverse</w>
-      <w>tril</w>
-      <w>trim</w>
-      <w>trim.default</w>
-      <w>trimEnds</w>
-      <w>trimLRPatterns</w>
-      <w>trimSum</w>
-      <w>trimTails</w>
-      <w>trimTailw</w>
-      <w>trimWhiteSpace</w>
-      <w>trimcluster</w>
-      <w>trimesh</w>
-      <w>trimkmeans</w>
-      <w>trimod</w>
-      <w>trimws</w>
-      <w>trind.generator</w>
-      <w>trinucleotideFrequency</w>
-      <w>triogram.fidelity</w>
-      <w>triogram.penalty</w>
-      <w>triplet</w>
-      <w>tritan</w>
-      <w>tritanomaly_cvd</w>
-      <w>triu</w>
-      <w>trls.influence</w>
-      <w>trmat</w>
-      <w>true</w>
-      <w>truegain</w>
-      <w>truehist</w>
-      <w>truelength</w>
-      <w>trunc</w>
-      <w>trunc.Date</w>
-      <w>trunc.POSIXt</w>
-      <w>truncPOSIXt</w>
-      <w>trunc_hms</w>
-      <w>trunc_mat</w>
-      <w>truncate</w>
-      <w>truncate.connection</w>
-      <w>try</w>
-      <w>try.flare</w>
-      <w>tryCatch</w>
-      <w>tryNULL</w>
-      <w>tryNew</w>
-      <w>try_capture_stack</w>
-      <w>try_default</w>
-      <w>try_silent</w>
-      <w>tryapply</w>
-      <w>tryget</w>
-      <w>trypanosome</w>
-      <w>ts</w>
-      <w>ts.intersect</w>
-      <w>ts.plot</w>
-      <w>ts.union</w>
-      <w>tsSmooth</w>
-      <w>tsboot</w>
-      <w>tsdiag</w>
-      <w>tsearch</w>
-      <w>tsearchn</w>
-      <w>tsne</w>
-      <w>tsort</w>
-      <w>tsp</w>
-      <w>tstrsplit</w>
-      <w>tsxpos</w>
-      <w>tt_alzh</w>
-      <w>tt_alzh_BA36</w>
-      <w>tt_alzh_BA44</w>
-      <w>ttest</w>
-      <w>ttheme</w>
-      <w>ttheme_default</w>
-      <w>ttheme_minimal</w>
-      <w>ttkbutton</w>
-      <w>ttkcheckbutton</w>
-      <w>ttkcombobox</w>
-      <w>ttkentry</w>
-      <w>ttkframe</w>
-      <w>ttklabel</w>
-      <w>ttklabelframe</w>
-      <w>ttkmenubutton</w>
-      <w>ttknotebook</w>
-      <w>ttkpanedwindow</w>
-      <w>ttkprogressbar</w>
-      <w>ttkradiobutton</w>
-      <w>ttkscale</w>
-      <w>ttkscrollbar</w>
-      <w>ttkseparator</w>
-      <w>ttksizegrip</w>
-      <w>ttkspinbox</w>
-      <w>ttktreeview</w>
-      <w>ttperm</w>
-      <w>tufte_handout</w>
-      <w>tukey.biweight</w>
-      <w>tukeyChi</w>
-      <w>tukeyPermutes</w>
-      <w>tukeyPsi1</w>
-      <w>tukeyT</w>
-      <w>tukeyTexture</w>
-      <w>tukeybiweight</w>
-      <w>tuna</w>
-      <w>tune</w>
-      <w>tune.control</w>
-      <w>tune.knn</w>
-      <w>tune.nnet</w>
-      <w>tune.randomForest</w>
-      <w>tune.rpart</w>
-      <w>tune.svm</w>
-      <w>tvdepfn</w>
-      <w>tw</w>
-      <w>tweak</w>
-      <w>tweedie</w>
-      <w>twindata</w>
-      <w>twitter_spambots</w>
-      <w>twlss</w>
-      <w>two.colors</w>
-      <w>two2one</w>
-      <w>twoClassSim</w>
-      <w>twoClassSummary</w>
-      <w>twoGroups</w>
-      <w>twoWayAlphabetFrequency</w>
-      <w>twoord.plot</w>
-      <w>twoord.stackplot</w>
-      <w>twostage</w>
-      <w>twostageCV</w>
-      <w>twostepsva.build</w>
-      <w>twowayFX</w>
-      <w>txhousing</w>
-      <w>tximport</w>
-      <w>txtInt</w>
-      <w>txtLabel</w>
-      <w>txtMergeLines</w>
-      <w>txtProgressBar</w>
-      <w>txtPval</w>
-      <w>txtRound</w>
-      <w>type</w>
-      <w>type.convert</w>
-      <w>typeIIIc</w>
-      <w>typeIIa</w>
-      <w>typeIIb</w>
-      <w>typeIIc</w>
-      <w>typeIId</w>
-      <w>typeIVc</w>
-      <w>typeIa</w>
-      <w>typeIas</w>
-      <w>typeIb</w>
-      <w>typeIbs</w>
-      <w>typeIc</w>
-      <w>typeIcs</w>
-      <w>typeId</w>
-      <w>typeIds</w>
-      <w>typeOfClass</w>
-      <w>typeOfClass.default</w>
-      <w>type_convert</w>
-      <w>type_sum</w>
-      <w>typeof</w>
-      <w>tz</w>
-      <w>u.Datumvonheute</w>
-      <w>u.assign0</w>
-      <w>u.boxplot.x</w>
-      <w>u.date</w>
-      <w>u.datumdecode</w>
-      <w>u.get0</w>
-      <w>u.log</w>
-      <w>u.sys</w>
-      <w>uccle</w>
-      <w>ucscGenomes</w>
-      <w>ucscSchema</w>
-      <w>ucscTableQuery</w>
-      <w>ucscTrackModes</w>
-      <w>ucsc_release</w>
-      <w>ucv</w>
-      <w>udca</w>
-      <w>ugraph</w>
-      <w>ugraphOld</w>
-      <w>uh</w>
-      <w>uiOutput</w>
-      <w>ui_code</w>
-      <w>ui_code_block</w>
-      <w>ui_done</w>
-      <w>ui_field</w>
-      <w>ui_info</w>
-      <w>ui_line</w>
-      <w>ui_nope</w>
-      <w>ui_oops</w>
-      <w>ui_path</w>
-      <w>ui_stop</w>
-      <w>ui_todo</w>
-      <w>ui_value</w>
-      <w>ui_warn</w>
-      <w>ui_yeah</w>
-      <w>uis</w>
-      <w>ultrametric</w>
-      <w>un86</w>
-      <w>unByteCode</w>
-      <w>unByteCodeAssign</w>
-      <w>unPaste</w>
-      <w>unRematchDefinition</w>
-      <w>unaligned</w>
-      <w>unattr</w>
-      <w>unbox</w>
-      <w>unbranch</w>
-      <w>unbuild.charmatrix</w>
-      <w>uncbind</w>
-      <w>uncerPlot</w>
-      <w>unclass</w>
-      <w>unclass_dend</w>
-      <w>unconstrain_pars</w>
-      <w>uncount</w>
-      <w>undebug</w>
-      <w>undebug.all</w>
-      <w>undebug.lr</w>
-      <w>undebug_fseq</w>
-      <w>undebugcall</w>
-      <w>underline</w>
-      <w>undim</w>
-      <w>undirected_graph</w>
-      <w>undoc</w>
-      <w>unemp</w>
-      <w>unemployment</w>
-      <w>unfactor</w>
-      <w>unfold.tree</w>
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-      <w>vectorField</w>
-      <w>vector_dc</w>
-      <w>venice</w>
-      <w>venice2</w>
-      <w>venn</w>
-      <w>venn.diagram</w>
-      <w>vennCounts</w>
-      <w>vennDiagram</w>
-      <w>vennPlot</w>
-      <w>vennlist</w>
-      <w>vennpie</w>
-      <w>vennplot</w>
-      <w>vennplot.peakfile</w>
-      <w>verbatimTextOutput</w>
-      <w>verbose</w>
-      <w>verifyAvailable</w>
-      <w>veronica</w>
-      <w>version</w>
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-      <w>veteran_lung_cancer</w>
-      <w>vgQ.bimin</w>
-      <w>vgQ.targetQ</w>
-      <w>vgQ.varimin</w>
-      <w>vgram</w>
-      <w>vgram.matrix</w>
-      <w>vi</w>
-      <w>viapply</w>
-      <w>view</w>
-      <w>viewApply</w>
-      <w>viewMaxs</w>
-      <w>viewMeans</w>
-      <w>viewMins</w>
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-      <w>vignette</w>
-      <w>vignetteDepends</w>
-      <w>vignetteEngine</w>
-      <w>vignetteMakefile</w>
-      <w>violinBy</w>
-      <w>violin_plot</w>
-      <w>vipor</w>
-      <w>viridis</w>
-      <w>viridis.map</w>
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-      <w>viridis_pal</w>
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-      <w>vis.gam</w>
-      <w>visible</w>
-      <w>visualize</w>
-      <w>vlapply</w>
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-      <w>vmatchPattern</w>
-      <w>vmembers</w>
-      <w>vmessage</w>
-      <w>vnapply</w>
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-      <w>xmlElementSummary</w>
-      <w>xmlElementsByTagName</w>
-      <w>xmlErrorCumulator</w>
-      <w>xmlEventHandler</w>
-      <w>xmlEventParse</w>
-      <w>xmlGetAttr</w>
-      <w>xmlHandler</w>
-      <w>xmlHashTree</w>
-      <w>xmlInternalTreeParse</w>
-      <w>xmlName</w>
-      <w>xmlNamespace</w>
-      <w>xmlNamespaceDefinitions</w>
-      <w>xmlNamespaces</w>
-      <w>xmlNativeTreeParse</w>
-      <w>xmlNode</w>
-      <w>xmlOutputBuffer</w>
-      <w>xmlOutputDOM</w>
-      <w>xmlPINode</w>
-      <w>xmlParent</w>
-      <w>xmlParse</w>
-      <w>xmlParseDoc</w>
-      <w>xmlParseString</w>
-      <w>xmlParserContextFunction</w>
-      <w>xmlRoot</w>
-      <w>xmlSApply</w>
-      <w>xmlSchemaParse</w>
-      <w>xmlSchemaValidate</w>
-      <w>xmlSearchNs</w>
-      <w>xmlSerializeHook</w>
-      <w>xmlSize</w>
-      <w>xmlSize.default</w>
-      <w>xmlSource</w>
-      <w>xmlSourceFunctions</w>
-      <w>xmlSourceSection</w>
-      <w>xmlStopParser</w>
-      <w>xmlStructuredStop</w>
-      <w>xmlTextNode</w>
-      <w>xmlToDataFrame</w>
-      <w>xmlToList</w>
-      <w>xmlToS4</w>
-      <w>xmlTree</w>
-      <w>xmlTreeParse</w>
-      <w>xmlValue</w>
-      <w>xmlXIncludes</w>
-      <w>xml_add_child</w>
-      <w>xml_add_parent</w>
-      <w>xml_add_sibling</w>
-      <w>xml_attr</w>
-      <w>xml_attrs</w>
-      <w>xml_cdata</w>
-      <w>xml_child</w>
-      <w>xml_children</w>
-      <w>xml_comment</w>
-      <w>xml_contents</w>
-      <w>xml_double</w>
-      <w>xml_dtd</w>
-      <w>xml_find_all</w>
-      <w>xml_find_chr</w>
-      <w>xml_find_first</w>
-      <w>xml_find_lgl</w>
-      <w>xml_find_num</w>
-      <w>xml_find_one</w>
-      <w>xml_has_attr</w>
-      <w>xml_integer</w>
-      <w>xml_length</w>
-      <w>xml_missing</w>
-      <w>xml_name</w>
-      <w>xml_new_document</w>
-      <w>xml_new_root</w>
-      <w>xml_ns</w>
-      <w>xml_ns_rename</w>
-      <w>xml_ns_strip</w>
-      <w>xml_parent</w>
-      <w>xml_parents</w>
-      <w>xml_path</w>
-      <w>xml_remove</w>
-      <w>xml_replace</w>
-      <w>xml_root</w>
-      <w>xml_serialize</w>
-      <w>xml_set_attr</w>
-      <w>xml_set_attrs</w>
-      <w>xml_set_name</w>
-      <w>xml_set_namespace</w>
-      <w>xml_set_text</w>
-      <w>xml_siblings</w>
-      <w>xml_structure</w>
-      <w>xml_text</w>
-      <w>xml_type</w>
-      <w>xml_unserialize</w>
-      <w>xml_url</w>
-      <w>xml_validate</w>
-      <w>xngettext</w>
-      <w>xopen</w>
-      <w>xor</w>
-      <w>xor.bit</w>
-      <w>xor.bitwhich</w>
-      <w>xor.default</w>
-      <w>xor.hexmode</w>
-      <w>xor.octmode</w>
-      <w>xpathApply</w>
-      <w>xpathSApply</w>
-      <w>xpdrows.data.frame</w>
-      <w>xpnd</w>
-      <w>xpred.rpart</w>
-      <w>xres</w>
-      <w>xscale</w>
-      <w>xscale.components.default</w>
-      <w>xscale.components.fractions</w>
-      <w>xscale.components.log</w>
-      <w>xscale.components.log10.3</w>
-      <w>xscale.components.log10ticks</w>
-      <w>xscale.components.logpower</w>
-      <w>xscale.components.subticks</w>
-      <w>xscat</w>
-      <w>xsimplex</w>
-      <w>xspline</w>
-      <w>xsplineGrob</w>
-      <w>xsplinePoints</w>
-      <w>xtable</w>
-      <w>xtableFtable</w>
-      <w>xtableLSMeans</w>
-      <w>xtableList</w>
-      <w>xtableMatharray</w>
-      <w>xtabs</w>
-      <w>xtfrm</w>
-      <w>xtfrm.AsIs</w>
-      <w>xtfrm.Date</w>
-      <w>xtfrm.POSIXct</w>
-      <w>xtfrm.POSIXlt</w>
-      <w>xtfrm.Surv</w>
-      <w>xtfrm.default</w>
-      <w>xtfrm.difftime</w>
-      <w>xtfrm.factor</w>
-      <w>xtfrm.numeric_version</w>
-      <w>xtfrm.zoo</w>
-      <w>xvcopy</w>
-      <w>xy.coords</w>
-      <w>xy.grid</w>
-      <w>xy.group</w>
-      <w>xy.unique.x</w>
-      <w>xy2indices</w>
-      <w>xyFromCell</w>
-      <w>xySortNoDupNoNA</w>
-      <w>xyTable</w>
-      <w>xyVector</w>
-      <w>xyinch</w>
-      <w>xyplot</w>
-      <w>xyplot.list</w>
-      <w>xyplot.ts</w>
-      <w>xyz.coords</w>
-      <w>xzfile</w>
-      <w>yDetails</w>
-      <w>yFromCell</w>
-      <w>yFromRow</w>
-      <w>yInch</w>
-      <w>yaml</w>
-      <w>yaml.load</w>
-      <w>yaml.load_file</w>
-      <w>yaml_front_matter</w>
-      <w>yan</w>
-      <w>yarn</w>
-      <w>yates</w>
-      <w>yates_setup</w>
-      <w>yaxisGrob</w>
-      <w>ycoef</w>
-      <w>yday</w>
-      <w>ydm</w>
-      <w>ydm_h</w>
-      <w>ydm_hm</w>
-      <w>ydm_hms</w>
-      <w>year</w>
-      <w>yearDays</w>
-      <w>yearmon</w>
-      <w>yearmon_trans</w>
-      <w>yearqtr</w>
-      <w>yearqtr_trans</w>
-      <w>years</w>
-      <w>yeast</w>
-      <w>yeastSEQCHR1</w>
-      <w>yellow</w>
-      <w>yield</w>
-      <w>yieldSize</w>
-      <w>yieldTabix</w>
-      <w>yinch</w>
-      <w>yjPower</w>
-      <w>yjPowerAxis</w>
-      <w>yj_trans</w>
-      <w>ylab</w>
-      <w>ylim</w>
-      <w>yline</w>
-      <w>ymatrix</w>
-      <w>ymax</w>
-      <w>ymd</w>
-      <w>ymd_h</w>
-      <w>ymd_hm</w>
-      <w>ymd_hms</w>
-      <w>ymin</w>
-      <w>ynbind</w>
-      <w>yq</w>
-      <w>yres</w>
-      <w>yscale</w>
-      <w>yscale.components.default</w>
-      <w>yscale.components.fractions</w>
-      <w>yscale.components.log</w>
-      <w>yscale.components.log10.3</w>
-      <w>yscale.components.log10ticks</w>
-      <w>yscale.components.logpower</w>
-      <w>yscale.components.subticks</w>
-      <w>yule</w>
-      <w>yule.cov</w>
-      <w>yule.time</w>
-      <w>z.ebam</w>
-      <w>z.find</w>
-      <w>zApply</w>
-      <w>zap_empty</w>
-      <w>zap_formats</w>
-      <w>zap_label</w>
-      <w>zap_labels</w>
-      <w>zap_missing</w>
-      <w>zap_widths</w>
-      <w>zapsmall</w>
-      <w>zeallot</w>
-      <w>zeroGrob</w>
-      <w>zero_range</w>
-      <w>zerodist</w>
-      <w>zerodist2</w>
-      <w>zeta</w>
-      <w>zi</w>
-      <w>ziP</w>
-      <w>zibreg</w>
-      <w>zip</w>
-      <w>zip_append</w>
-      <w>zip_list</w>
-      <w>zip_process</w>
-      <w>zipdown</w>
-      <w>ziplss</w>
-      <w>zipr</w>
-      <w>zipr_append</w>
-      <w>zipup</w>
-      <w>zlibbioc</w>
-      <w>zmisclassification.matrix</w>
-      <w>zo</w>
-      <w>zonal</w>
-      <w>zoo</w>
-      <w>zoom</w>
-      <w>zoomInPlot</w>
-      <w>zoomIntoRegion</w>
-      <w>zooreg</w>
-      <w>zscore</w>
-      <w>zscoreGamma</w>
-      <w>zscoreHyper</w>
-      <w>zscoreNBinom</w>
-      <w>zscoreT</w>
-    </words>
-  </dictionary>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/R_User_Library.xml b/.idea/libraries/R_User_Library.xml
deleted file mode 100644
index 71f5ff7..0000000
--- a/.idea/libraries/R_User_Library.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<component name="libraryTable">
-  <library name="R User Library">
-    <CLASSES />
-    <SOURCES />
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 903a29c..0000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="JavaScriptSettings">
-    <option name="languageLevel" value="ES6" />
-  </component>
-  <component name="NodePackageJsonFileManager">
-    <packageJsonPaths />
-  </component>
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6 (scaden)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index b3fa723..0000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/scaden.iml" filepath="$PROJECT_DIR$/.idea/scaden.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/scaden.iml b/.idea/scaden.iml
deleted file mode 100644
index 3a4807d..0000000
--- a/.idea/scaden.iml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$" />
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="library" name="R Skeletons" level="application" />
-    <orderEntry type="library" name="R User Library" level="project" />
-  </component>
-  <component name="TestRunnerService">
-    <option name="PROJECT_TEST_RUNNER" value="Unittests" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 94a25f7..0000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
deleted file mode 100644
index e2a4630..0000000
--- a/conda.recipe/meta.yaml
+++ /dev/null
@@ -1,55 +0,0 @@
-{% set data = load_setup_py_data() %}
-
-package:
-  name: 'scaden'
-  version: {{ data.get('version') }}
-
-source:
-  path: ..
-
-build:
-  number: 0
-  script: pip install . --no-deps --ignore-installed --no-cache-dir
-  noarch: python
-  script_env:
-    - COVERAGE_DIR
-
-requirements:
-  host:
-    - python {{ python }}
-    - pip
-    - twine
-  run:
-    - python {{ python }}
-    - pandas
-    - numpy
-    - scikit-learn
-    - anndata
-    - tensorflow >=2.0
-    - scanpy
-    - tqdm
-    - click
-
-test:
-  requires:
-    - coverage
-#  source_files:
-#    - .coveragerc
-  commands:
-    - scaden --help
-
-
-# tests fail because of tesnorflow, commenting out
-#test:
-#  commands:
-#    - scaden --help
-
-about:
-  home: https://github.com/KevinMenden/scaden
-  license: MIT
-  summary: Cell type deconvolution using single cell data
-
-extra:
-  skip-lints:
-    - missing_tests
-
diff --git a/environment.yml b/environment.yml
index c96be71..515d843 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,6 +5,6 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - scaden=0.9.0=py_0
+  - scaden=0.9.4=py_0
 prefix: /home/kevin/anaconda3/envs/scaden
 
diff --git a/scaden/__init__.py b/scaden/__init__.py
index e69de29..415b1b5 100644
--- a/scaden/__init__.py
+++ b/scaden/__init__.py
@@ -0,0 +1,3 @@
+import pkg_resources
+
+__version__ = pkg_resources.get_distribution("scaden").version
\ No newline at end of file
diff --git a/scaden/__main__.py b/scaden/__main__.py
index bbad801..94c0286 100644
--- a/scaden/__main__.py
+++ b/scaden/__main__.py
@@ -1,5 +1,148 @@
-from scaden.cli import main
+import click
+import scaden
+from scaden.scaden_main import training, prediction, processing
+"""
+
+author: Kevin Menden
+
+This is the main file for executing the Scaden program.
+"""
+
+
+
+def main():
+    text = """
+     ____                _            
+    / ___|  ___ __ _  __| | ___ _ __  
+    \___ \ / __/ _` |/ _` |/ _ \ '_ \ 
+     ___) | (_| (_| | (_| |  __/ | | |
+    |____/ \___\__,_|\__,_|\___|_| |_|
+
+    """
+    click.echo(click.style(text, fg='blue'))
+    cli()
+
 
 if __name__ == '__main__':
     main()
 
+
+"""
+Set up the command line client with different commands to execute
+"""
+
+
+@click.group()
+@click.version_option(scaden.__version__)
+def cli():
+    pass
+
+"""
+Training mode
+"""
+@cli.command()
+@click.argument(
+    'data_path',
+    type = click.Path(exists=True),
+    required = True,
+    metavar = '<training data>'
+)
+@click.option(
+    '--train_datasets',
+    default = '',
+    help = 'Datasets used for training. Uses all by default.'
+)
+@click.option(
+    '--model_dir',
+    default = "./",
+    help = 'Path to store the model in'
+)
+@click.option(
+    '--batch_size',
+    default = 128,
+    help = 'Batch size to use for training. Default: 128'
+)
+@click.option(
+    '--learning_rate',
+    default = 0.0001,
+    help = 'Learning rate used for training. Default: 0.0001'
+)
+@click.option(
+    '--steps',
+    default = 5000,
+    help = 'Number of training steps'
+)
+def train(data_path, train_datasets, model_dir, batch_size, learning_rate, steps):
+    """ Train a cdn model """
+    training(data_path=data_path,
+                      train_datasets=train_datasets,
+                      model_dir=model_dir,
+                      batch_size=batch_size,
+                      learning_rate=learning_rate,
+                      num_steps=steps)
+
+
+"""
+Prediction mode
+"""
+@cli.command()
+@click.argument(
+    'data_path',
+    type = click.Path(exists=True),
+    required = True,
+    metavar = '<prediction data>'
+)
+@click.option(
+    '--model_dir',
+    default = "./",
+    help = 'Path to trained model'
+)
+@click.option(
+    '--outname',
+    default = "scaden_predictions.txt",
+    help = 'Name of predictions file.'
+)
+def predict(data_path, model_dir, outname):
+    """ cdn prediction using a trained model """
+    prediction(model_dir=model_dir,
+                        data_path=data_path,
+                        out_name=outname)
+
+
+
+"""
+Processing mode
+"""
+@cli.command()
+@click.argument(
+    'data_path',
+    type = click.Path(exists=True),
+    required = True,
+    metavar = '<training dataset to be processed>'
+)
+@click.argument(
+    'prediction_data',
+    type = click.Path(exists=True),
+    required = True,
+    metavar = '<data for prediction>'
+)
+@click.option(
+    '--processed_path',
+    default = "processed.h5ad",
+    help = 'Path of processed file. Must end with .h5ad'
+)
+@click.option(
+    '--var_cutoff',
+    default = 0.1,
+    help = 'Filter out genes with a variance less than the specified cutoff. A low cutoff is recommended,'
+           'this should only remove genes that are obviously uninformative.'
+)
+def process(data_path, prediction_data, processed_path, var_cutoff):
+    """ Process a dataset for training """
+    processing(data_path=prediction_data,
+                        training_data=data_path,
+                        processed_path=processed_path,
+                        var_cutoff=var_cutoff
+               )
+
+
diff --git a/scaden/cli.py b/scaden/cli.py
deleted file mode 100644
index f4ab6ba..0000000
--- a/scaden/cli.py
+++ /dev/null
@@ -1,138 +0,0 @@
-"""
-cdn Command Line Interface
-author: Kevin Menden, DZNE Tübingen
-
-This is the main file for executing the cdn program.
-"""
-
-# imports
-import click
-import scaden
-from scaden.scaden_main import training, prediction, processing
-
-@click.group()
-@click.version_option('1.0.0')
-def cli():
-    pass
-
-
-"""
-Training mode
-"""
-@cli.command()
-@click.argument(
-    'data_path',
-    type = click.Path(exists=True),
-    required = True,
-    metavar = '<training data>'
-)
-@click.option(
-    '--train_datasets',
-    default = '',
-    help = 'Datasets used for training. Uses all by default.'
-)
-@click.option(
-    '--model_dir',
-    default = "./",
-    help = 'Path to store the model in'
-)
-@click.option(
-    '--batch_size',
-    default = 128,
-    help = 'Batch size to use for training. Default: 128'
-)
-@click.option(
-    '--learning_rate',
-    default = 0.0001,
-    help = 'Learning rate used for training. Default: 0.0001'
-)
-@click.option(
-    '--steps',
-    default = 20000,
-    help = 'Number of training steps'
-)
-def train(data_path, train_datasets, model_dir, batch_size, learning_rate, steps):
-    """ Train a cdn model """
-    training(data_path=data_path,
-                      train_datasets=train_datasets,
-                      model_dir=model_dir,
-                      batch_size=batch_size,
-                      learning_rate=learning_rate,
-                      num_steps=steps)
-
-
-"""
-Prediction mode
-"""
-@cli.command()
-@click.argument(
-    'data_path',
-    type = click.Path(exists=True),
-    required = True,
-    metavar = '<prediction data>'
-)
-@click.option(
-    '--model_dir',
-    default = "./",
-    help = 'Path to trained model'
-)
-@click.option(
-    '--outname',
-    default = "scaden_predictions.txt",
-    help = 'Name of predictions file.'
-)
-def predict(data_path, model_dir, outname):
-    """ cdn prediction using a trained model """
-    prediction(model_dir=model_dir,
-                        data_path=data_path,
-                        out_name=outname)
-
-
-
-"""
-Processing mode
-"""
-@cli.command()
-@click.argument(
-    'data_path',
-    type = click.Path(exists=True),
-    required = True,
-    metavar = '<training dataset to be processed>'
-)
-@click.argument(
-    'prediction_data',
-    type = click.Path(exists=True),
-    required = True,
-    metavar = '<data for prediction>'
-)
-@click.option(
-    '--processed_path',
-    default = "processed.h5ad",
-    help = 'Path of processed file. Must end with .h5ad'
-)
-@click.option(
-    '--var_cutoff',
-    default = 0.1,
-    help = 'Filter out genes with a variance less than the specified cutoff. A low cutoff is recommended,'
-           'this should only remove genes that are obviously uninformative.'
-)
-def process(data_path, prediction_data, processed_path, var_cutoff):
-    """ Process a dataset for training """
-    processing(data_path=prediction_data,
-                        training_data=data_path,
-                        processed_path=processed_path,
-                        var_cutoff=var_cutoff
-               )
-
-def main():
-    text = """
-     ____                _            
-    / ___|  ___ __ _  __| | ___ _ __  
-    \___ \ / __/ _` |/ _` |/ _ \ '_ \ 
-     ___) | (_| (_| | (_| |  __/ | | |
-    |____/ \___\__,_|\__,_|\___|_| |_|
-
-    """
-    click.echo(click.style(text, fg='blue'))
-    cli()
-
diff --git a/scripts/scaden b/scripts/scaden
deleted file mode 100755
index 54b3faa..0000000
--- a/scripts/scaden
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env python
-
-"""
-cdn Command Line Interface
-author: Kevin Menden, DZNE Tübingen
-
-This is the main file for executing the cdn program.
-"""
-
-from scaden.cli import main
-
-if __name__ == '__main__':
-    main()
-
diff --git a/setup.py b/setup.py
index c4d5c09..cb06aa8 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@
     author_email='kevin.menden@t-online.de',
     url='https://github.com/KevinMenden/scaden',
     license="MIT License",
-    scripts=['scripts/scaden'],
+    entry_points={"console_scripts": ["scaden=scaden.__main__:main"]},
     packages=find_packages(),
     include_package_data=True,
     python_requires='>3.6.0',

From 33d27e68ce80746f6aaf5eae95bade2ce5e15df1 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 07:44:50 +0100
Subject: [PATCH 2/9] got rid of scaden_main.py

---
 .vscode/settings.json                         |  3 +
 CHANGELOG.md                                  |  8 +-
 scaden/scaden/__init__.py                     |  0
 scaden/scaden/prediction.py                   | 82 +++++++++++++++++++
 scaden/scaden/processing.py                   | 37 +++++++++
 scaden/{scaden_main.py => scaden/training.py} | 74 +----------------
 6 files changed, 129 insertions(+), 75 deletions(-)
 create mode 100644 .vscode/settings.json
 create mode 100644 scaden/scaden/__init__.py
 create mode 100644 scaden/scaden/prediction.py
 create mode 100644 scaden/scaden/processing.py
 rename scaden/{scaden_main.py => scaden/training.py} (52%)

diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..79b73ce
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "python.pythonPath": "/home/kevin/anaconda3/envs/scaden/bin/python"
+}
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a7a644..bc2d954 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Scaden Changelog
 
+## v0.9.5
+
+* changed CLI calling
+
 ## v0.9.4
 
 * fixed dependencies (added python>=3.6 requirement)
@@ -21,10 +25,10 @@
 
 ## v0.9.0   
 
-Initial release of the CDN deconvolution package.
+Initial release of the Scaden deconvolution package.
 
 Commands:
 
 * `scaden process`: Process a training dataset for training
-* `scaden train`: Train a CDN model
+* `scaden train`: Train a Scaden model
 * `scaden predict`: Predict cell type compositions of a given sample
\ No newline at end of file
diff --git a/scaden/scaden/__init__.py b/scaden/scaden/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/scaden/scaden/prediction.py b/scaden/scaden/prediction.py
new file mode 100644
index 0000000..01defd2
--- /dev/null
+++ b/scaden/scaden/prediction.py
@@ -0,0 +1,82 @@
+"""
+scaden Main functionality
+
+Contains code to
+- process a training datasets
+- train a model
+- perform predictions
+
+"""
+
+# Imports
+import tensorflow as tf
+from anndata import read_h5ad
+from scaden.model.architectures import architectures
+from scaden.model.scaden import Scaden
+
+"""
+PARAMETERS
+"""
+# ==========================================#
+
+# Extract architectures
+M256_HIDDEN_UNITS = architectures['m256'][0]
+M512_HIDDEN_UNITS = architectures['m512'][0]
+M1024_HIDDEN_UNITS = architectures['m1024'][0]
+M256_DO_RATES = architectures['m256'][1]
+M512_DO_RATES = architectures['m512'][1]
+M1024_DO_RATES = architectures['m1024'][1]
+
+
+# ==========================================#
+
+
+def prediction(model_dir, data_path, out_name):
+    """
+    Perform prediction using a trained scaden ensemble
+    :param model_dir: the directory containing the models
+    :param data_path: the path to the gene expression file
+    :param out_name: name of the output prediction file
+    :return:
+    """
+
+    # Small model predictions
+    tf.compat.v1.reset_default_graph()
+    with tf.compat.v1.Session() as sess:
+        cdn256 = Scaden(sess=sess,
+                     model_dir=model_dir + "/m256",
+                     model_name='m256')
+        cdn256.hidden_units = M256_HIDDEN_UNITS
+        cdn256.do_rates = M256_DO_RATES
+
+        # Predict ratios
+        preds_256 = cdn256.predict(input_path=data_path,  out_name='scaden_predictions_m256.txt')
+
+
+    # Mid model predictions
+    tf.compat.v1.reset_default_graph()
+    with tf.compat.v1.Session() as sess:
+        cdn512 = Scaden(sess=sess,
+                     model_dir=model_dir+"/m512",
+                     model_name='m512')
+        cdn512.hidden_units = M512_HIDDEN_UNITS
+        cdn512.do_rates = M512_DO_RATES
+
+        # Predict ratios
+        preds_512 = cdn512.predict(input_path=data_path, out_name='scaden_predictions_m512.txt')
+
+    # Large model predictions
+    tf.compat.v1.reset_default_graph()
+    with tf.compat.v1.Session() as sess:
+        cdn1024 = Scaden(sess=sess,
+                      model_dir=model_dir+"/m1024",
+                      model_name='m1024')
+        cdn1024.hidden_units = M1024_HIDDEN_UNITS
+        cdn1024.do_rates = M1024_DO_RATES
+
+        # Predict ratios
+        preds_1024 = cdn1024.predict(input_path=data_path, out_name='scaden_predictions_m1024.txt')
+
+    # Average predictions
+    preds = (preds_256 + preds_512 + preds_1024) / 3
+    preds.to_csv(out_name, sep="\t")
diff --git a/scaden/scaden/processing.py b/scaden/scaden/processing.py
new file mode 100644
index 0000000..3debd4c
--- /dev/null
+++ b/scaden/scaden/processing.py
@@ -0,0 +1,37 @@
+"""
+scaden Main functionality
+
+Contains code to
+- process a training datasets
+- train a model
+- perform predictions
+
+"""
+
+# Imports
+import tensorflow as tf
+from anndata import read_h5ad
+from scaden.model.functions import get_signature_genes, preprocess_h5ad_data
+
+"""
+PARAMETERS
+"""
+# ==========================================#
+
+def processing(data_path, training_data, processed_path, var_cutoff):
+    """
+    Process a training dataset to contain only the genes also available in the prediction data
+    :param data_path: path to prediction data
+    :param training_data: path to training data (h5ad file)
+    :param processed_path: name of processed file
+    :return:
+    """
+    # Get the common genes (signature genes)
+    raw_input = read_h5ad(training_data)
+    sig_genes_complete = list(raw_input.var_names)
+    sig_genes = get_signature_genes(input_path=data_path, sig_genes_complete=sig_genes_complete, var_cutoff=var_cutoff)
+
+    # Pre-process data with new signature genes
+    preprocess_h5ad_data(raw_input_path=training_data,
+                         processed_path=processed_path,
+                         sig_genes=sig_genes)
diff --git a/scaden/scaden_main.py b/scaden/scaden/training.py
similarity index 52%
rename from scaden/scaden_main.py
rename to scaden/scaden/training.py
index e09acc1..538863b 100644
--- a/scaden/scaden_main.py
+++ b/scaden/scaden/training.py
@@ -13,7 +13,6 @@
 from anndata import read_h5ad
 from scaden.model.architectures import architectures
 from scaden.model.scaden import Scaden
-from scaden.model.functions import get_signature_genes, preprocess_h5ad_data
 
 """
 PARAMETERS
@@ -28,7 +27,6 @@
 M512_DO_RATES = architectures['m512'][1]
 M1024_DO_RATES = architectures['m1024'][1]
 
-
 # ==========================================#
 
 
@@ -94,74 +92,4 @@ def training(data_path, train_datasets, model_dir, batch_size, learning_rate, nu
         cdn1024.train(input_path=data_path, train_datasets=train_datasets)
     del cdn1024
 
-    print("Training finished.")
-
-
-def prediction(model_dir, data_path, out_name):
-    """
-    Perform prediction using a trained scaden ensemble
-    :param model_dir: the directory containing the models
-    :param data_path: the path to the gene expression file
-    :param out_name: name of the output prediction file
-    :return:
-    """
-
-    # Small model predictions
-    tf.compat.v1.reset_default_graph()
-    with tf.compat.v1.Session() as sess:
-        cdn256 = Scaden(sess=sess,
-                     model_dir=model_dir + "/m256",
-                     model_name='m256')
-        cdn256.hidden_units = M256_HIDDEN_UNITS
-        cdn256.do_rates = M256_DO_RATES
-
-        # Predict ratios
-        preds_256 = cdn256.predict(input_path=data_path,  out_name='scaden_predictions_m256.txt')
-
-
-    # Mid model predictions
-    tf.compat.v1.reset_default_graph()
-    with tf.compat.v1.Session() as sess:
-        cdn512 = Scaden(sess=sess,
-                     model_dir=model_dir+"/m512",
-                     model_name='m512')
-        cdn512.hidden_units = M512_HIDDEN_UNITS
-        cdn512.do_rates = M512_DO_RATES
-
-        # Predict ratios
-        preds_512 = cdn512.predict(input_path=data_path, out_name='scaden_predictions_m512.txt')
-
-    # Large model predictions
-    tf.compat.v1.reset_default_graph()
-    with tf.compat.v1.Session() as sess:
-        cdn1024 = Scaden(sess=sess,
-                      model_dir=model_dir+"/m1024",
-                      model_name='m1024')
-        cdn1024.hidden_units = M1024_HIDDEN_UNITS
-        cdn1024.do_rates = M1024_DO_RATES
-
-        # Predict ratios
-        preds_1024 = cdn1024.predict(input_path=data_path, out_name='scaden_predictions_m1024.txt')
-
-    # Average predictions
-    preds = (preds_256 + preds_512 + preds_1024) / 3
-    preds.to_csv(out_name, sep="\t")
-
-
-def processing(data_path, training_data, processed_path, var_cutoff):
-    """
-    Process a training dataset to contain only the genes also available in the prediction data
-    :param data_path: path to prediction data
-    :param training_data: path to training data (h5ad file)
-    :param processed_path: name of processed file
-    :return:
-    """
-    # Get the common genes (signature genes)
-    raw_input = read_h5ad(training_data)
-    sig_genes_complete = list(raw_input.var_names)
-    sig_genes = get_signature_genes(input_path=data_path, sig_genes_complete=sig_genes_complete, var_cutoff=var_cutoff)
-
-    # Pre-process data with new signature genes
-    preprocess_h5ad_data(raw_input_path=training_data,
-                         processed_path=processed_path,
-                         sig_genes=sig_genes)
+    print("Training finished.")
\ No newline at end of file

From cbd62f1bb308e5e1a0e6d77a2d1bb997a02fe3f9 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 09:22:08 +0100
Subject: [PATCH 3/9] added 'scaden simuate' functionality

---
 README.md                                |   2 +
 scaden/__main__.py                       |  59 ++++++-
 scaden/preprocessing/bulk_simulation.py  | 191 ++++++++++++-----------
 scaden/preprocessing/create_h5ad_file.py | 132 +++++++---------
 scaden/preprocessing/simulate.py         |  27 ++++
 5 files changed, 243 insertions(+), 168 deletions(-)
 create mode 100644 scaden/preprocessing/simulate.py

diff --git a/README.md b/README.md
index f8ec1da..38151de 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,7 @@
 ![Scaden](docs/img/scaden_logo.png)
 
+![MIT](https://anaconda.org/bioconda/scaden/badges/license.svg)
+![Install with Bioconda](https://anaconda.org/bioconda/scaden/badges/installer/conda.svg)
 ## Single-cell assisted deconvolutional network
 
 Scaden is a deep-learning based algorithm for cell type deconvolution of bulk RNA-seq samples. It was developed 
diff --git a/scaden/__main__.py b/scaden/__main__.py
index 94c0286..b25b356 100644
--- a/scaden/__main__.py
+++ b/scaden/__main__.py
@@ -1,6 +1,9 @@
 import click
 import scaden
-from scaden.scaden_main import training, prediction, processing
+from scaden.scaden.training import training
+from scaden.scaden.prediction import prediction
+from scaden.scaden.processing import processing
+from scaden.preprocessing.simulate import simulation
 """
 
 author: Kevin Menden
@@ -73,7 +76,7 @@ def cli():
     help = 'Number of training steps'
 )
 def train(data_path, train_datasets, model_dir, batch_size, learning_rate, steps):
-    """ Train a cdn model """
+    """ Train a Scaden model """
     training(data_path=data_path,
                       train_datasets=train_datasets,
                       model_dir=model_dir,
@@ -103,7 +106,7 @@ def train(data_path, train_datasets, model_dir, batch_size, learning_rate, steps
     help = 'Name of predictions file.'
 )
 def predict(data_path, model_dir, outname):
-    """ cdn prediction using a trained model """
+    """ Predict cell type composition using a trained Scaden model"""
     prediction(model_dir=model_dir,
                         data_path=data_path,
                         out_name=outname)
@@ -145,4 +148,54 @@ def process(data_path, prediction_data, processed_path, var_cutoff):
                         var_cutoff=var_cutoff
                )
 
+"""
+Simulate dataset
+"""
+@cli.command()
+@click.option(
+    '--out', '-o',
+    default = './',
+    help = "Directory to store output files in"
+)
+@click.option(
+    '--data', '-d',
+    default = '.',
+    help = "Path to scRNA-seq dataset(s)"
+)
+@click.option(
+    '--cells', '-c',
+    default = 100,
+    help = "Number of cells per sample [default: 100]"
+)
+@click.option(
+    '--n_samples', '-n',
+    default = 1000,
+    help = "Number of samples to simulate [default: 1000]"
+)
+@click.option(
+    '--pattern', 
+    default = "*_norm_counts_all.txt",
+    help = "File pattern to recognize your processed scRNA-seq count files"
+)
+@click.option(
+    '--unknown', '-m',
+    default = ['unkown'],
+    help = "Specifiy cell types to merge into the unknown category."
 
+)
+@click.option(
+    '--prefix', '-p',
+    default = "data",
+    help = "Prefix to append to training .h5ad file [default: data]"
+)
+def simulate(out, data, cells, n_samples, pattern, unknown, prefix):
+    """ Create artificial bulk RNA-seq data from scRNA-seq dataset(s)"""
+    simulation(
+        simulate_dir=out, 
+        data_dir=data, 
+        sample_size=cells, 
+        num_samples=n_samples, 
+        pattern=pattern, 
+        unknown_celltypes=unknown, 
+        out_prefix=prefix
+        )
diff --git a/scaden/preprocessing/bulk_simulation.py b/scaden/preprocessing/bulk_simulation.py
index dfeb78a..c1d20f6 100644
--- a/scaden/preprocessing/bulk_simulation.py
+++ b/scaden/preprocessing/bulk_simulation.py
@@ -8,6 +8,8 @@
 import os
 import argparse
 import gc
+from tqdm import tqdm
+
 
 def create_fractions(no_celltypes):
     """
@@ -36,7 +38,9 @@ def create_subsample(x, y, sample_size, celltypes, available_celltypes, sparse=F
 
     if sparse:
         no_keep = np.random.randint(1, len(available_celltypes))
-        keep = np.random.choice(list(range(len(available_celltypes))), size=no_keep, replace=False)
+        keep = np.random.choice(
+            list(range(len(available_celltypes))), size=no_keep, replace=False
+        )
         available_celltypes = [available_celltypes[i] for i in keep]
 
     no_avail_cts = len(available_celltypes)
@@ -48,14 +52,14 @@ def create_subsample(x, y, sample_size, celltypes, available_celltypes, sparse=F
 
     # Make complete fracions
     fracs_complete = [0] * len(celltypes)
-    for i,act in enumerate(available_celltypes):
+    for i, act in enumerate(available_celltypes):
         idx = celltypes.index(act)
         fracs_complete[idx] = fracs[i]
 
     artificial_samples = []
     for i in range(no_avail_cts):
         ct = available_celltypes[i]
-        cells_sub = x.loc[np.array(y['Celltype'] == ct),:]
+        cells_sub = x.loc[np.array(y["Celltype"] == ct), :]
         cells_fraction = np.random.randint(0, cells_sub.shape[0], samp_fracs[i])
         cells_sub = cells_sub.iloc[cells_fraction, :]
         artificial_samples.append(cells_sub)
@@ -80,33 +84,34 @@ def create_subsample_dataset(x, y, sample_size, celltypes, no_samples):
     X = []
     Y = []
 
-    available_celltypes = list(set(y['Celltype'].tolist()))
+    available_celltypes = list(set(y["Celltype"].tolist()))
 
     # Create normal samples
-    for i in range(no_samples):
-        sample, label = create_subsample(x, y, sample_size, celltypes, available_celltypes)
+    pbar = tqdm(range(no_samples))
+    pbar.set_description(desc="Normal samples")
+    for _ in pbar:
+        sample, label = create_subsample(
+            x, y, sample_size, celltypes, available_celltypes
+        )
         X.append(sample)
         Y.append(label)
-        if i % 1 == 0:
-            print(i)
 
     # Create sparse samples
     n_sparse = int(no_samples)
-    #n_sparse = 0
-    for i in range(n_sparse):
-        sample, label = create_subsample(x, y, sample_size, celltypes, available_celltypes, sparse=True)
+    pbar = tqdm(range(n_sparse))
+    pbar.set_description(desc="Sparse samples")
+    for _ in pbar:
+        sample, label = create_subsample(
+            x, y, sample_size, celltypes, available_celltypes, sparse=True
+        )
         X.append(sample)
         Y.append(label)
-        if i % 1 == 0:
-            print(i)
     X = pd.concat(X, axis=1).T
     Y = pd.DataFrame(Y, columns=celltypes)
 
-    # Shuffle
-    #X, Y = shuffle_dataset(X, Y)
-
     return (X, Y)
 
+
 def filter_for_celltypes(x, y, celltypes):
     """
     Filter data for cells belonging to specified celltypes
@@ -115,14 +120,13 @@ def filter_for_celltypes(x, y, celltypes):
     :param celltypes:
     :return:
     """
-    cts = list(y['Celltype'])
+    cts = list(y["Celltype"])
     keep = [elem in celltypes for elem in cts]
     x = x.loc[keep, :]
     y = y.loc[keep, :]
     return (x, y)
 
 
-
 def shuffle_dataset(x, y):
     """
     Shuffle dataset while keeping x and y in synch
@@ -135,6 +139,7 @@ def shuffle_dataset(x, y):
     y_shuff = y.reindex(idx)
     return (x_shuff, y_shuff)
 
+
 def filter_matrix_signature(mat, genes):
     """
     Filter expression matrix using given genes
@@ -154,6 +159,7 @@ def filter_matrix_signature(mat, genes):
     mat = mat[genes]
     return mat
 
+
 def load_dataset(name, dir, pattern):
     """
     Load a dataset given its name and the directory
@@ -168,6 +174,7 @@ def load_dataset(name, dir, pattern):
     y = pd.read_table(dir + name + "_celltypes.txt")
     return (x, y)
 
+
 def merge_unkown_celltypes(y, unknown_celltypes):
     """
     Merge all unknown celltypes together
@@ -176,25 +183,27 @@ def merge_unkown_celltypes(y, unknown_celltypes):
     :param unknown_celltypes:
     :return:
     """
-    celltypes = list(y['Celltype'])
+    celltypes = list(y["Celltype"])
     new_celltypes = ["Unknown" if x in unknown_celltypes else x for x in celltypes]
-    y['Celltype'] = new_celltypes
+    y["Celltype"] = new_celltypes
     return y
 
+
 def collect_celltypes(ys):
     """
     Collect all available celltypes given all dataset labels
     :param ys: list of dataset labels
     :return: list of available celltypes
     """
-    ct_list = [list(set(y['Celltype'].tolist())) for y in ys]
+    ct_list = [list(set(y["Celltype"].tolist())) for y in ys]
     celltypes = set()
     for ct in ct_list:
         celltypes = celltypes.union(set(ct))
     celltypes = list(celltypes)
     return celltypes
 
-def get_common_genes(xs, type='intersection'):
+
+def get_common_genes(xs, type="intersection"):
     """
     Get common genes for all matrices xs
     Can either be the union or the intersection (default) of all genes
@@ -207,21 +216,22 @@ def get_common_genes(xs, type='intersection'):
 
     genes = [set(g) for g in genes]
     com_genes = genes[0]
-    if type=='union':
+    if type == "union":
         for gi in range(1, len(genes)):
             com_genes = com_genes.union(genes[gi])
-    elif type=='intersection':
+    elif type == "intersection":
         for gi in range(1, len(genes)):
             com_genes = com_genes.intersection(genes[gi])
 
     else:
-        exit('Wrong type selected to get common genes. Exiting.')
+        exit("Wrong type selected to get common genes. Exiting.")
 
     if len(com_genes) == 0:
         exit("No common genes found. Exiting.")
 
     return list(com_genes)
 
+
 def generate_signature(x, y):
     """
     Generate signature of matrix using celltypes y
@@ -231,9 +241,9 @@ def generate_signature(x, y):
     """
 
     signature_matrix = []
-    celltypes = list(set(y['Celltype']))
+    celltypes = list(set(y["Celltype"]))
     for ct in celltypes:
-        ct_exp = x.loc[np.array(y['Celltype'] == ct), :]
+        ct_exp = x.loc[np.array(y["Celltype"] == ct), :]
         ct_exp = ct_exp.mean(axis=0)
         signature_matrix.append(ct_exp)
 
@@ -242,68 +252,65 @@ def generate_signature(x, y):
     return signature_matrix
 
 
-"""
-Main Section
-"""
-
-parser = argparse.ArgumentParser()
-parser.add_argument("--cells", type=int, help="Number of cells to use for each sample.", default=100)
-parser.add_argument("--samples", "-n", type=int, help="Total number of samples to create for each dataset.", default=8000)
-parser.add_argument("--data", type=str, help="Directory containg the datsets", default="/home/kevin/deepcell_project/datasets/PBMCs/processed_data")
-parser.add_argument("--out", type=str, help="Output directory", default="./")
-parser.add_argument("--pattern", type=str, help="File pattern to use for getting the datasets (default: *_norm_counts_all.txt", default="*_norm_counts_all.txt")
-parser.add_argument("--unknown", type=str, help="All cell types to group into unknown", nargs='+', default=['Unknown', 'Unkown', 'Neutrophil', 'Dendritic'])
-args = parser.parse_args()
-
-# Parameters
-sample_size = args.cells
-num_samples = int(args.samples / 2) # divide by two so half is sparse and half is normal samples
-data_path = args.data
-out_dir = args.out
-pattern = args.pattern
-unknown_celltypes = args.unknown
-
-
-# List available datasets
-files = glob.glob(data_path + pattern)
-files = [os.path.basename(x) for x in files]
-datasets = [x.split("_")[0] for x in files]
-print("Datasets: " + str(datasets))
-
-# Load datasets
-xs, ys = [], []
-for i, n in enumerate(datasets):
-    x, y = load_dataset(n, data_path, pattern=pattern)
-    xs.append(x)
-    ys.append(y)
-
-# Get common gene list
-all_genes = get_common_genes(xs, type='intersection')
-print("No. of common genes: " + str(len(all_genes)))
-xs = [filter_matrix_signature(m, all_genes) for m in xs]
-
-# Merge unknown celltypes
-print("Merging unknown cell types: " + str(unknown_celltypes))
-for i in range(len(ys)):
-    ys[i] = merge_unkown_celltypes(ys[i], unknown_celltypes)
-
-# Collect all available celltypes
-celltypes = collect_celltypes(ys)
-print("Available celltypes: " + str(celltypes))
-pd.DataFrame(celltypes).to_csv(out_dir + "celltypes.txt", sep="\t")
-
-# Create signature matrices (for use with Cibersort)
-sig_mats = []
-for i in range(len(xs)):
-    sm = generate_signature(xs[i], ys[i])
-    sig_mats.append(sm)
-
-# Create datasets
-for i in range(len(xs)):
-    print("Subsampling " + datasets[i] + "...")
-    tmpx, tmpy = create_subsample_dataset(xs[i], ys[i], sample_size, celltypes, num_samples)
-    tmpx.to_csv(out_dir + datasets[i] + "_samples.txt", sep="\t", index=False)
-    tmpy.to_csv(out_dir + datasets[i] + "_labels.txt", sep="\t", index=False)
-    gc.collect()
-
-print("Finished!")
+def simulate_bulk(
+    sample_size, num_samples, data_path, out_dir, pattern, unknown_celltypes
+):
+    """
+    Simulate artificial bulk samples from single cell datasets
+    :param sample_size: number of cells per sample
+    :param num_samples: number of sample to simulate
+    :param data_path: path to the data directory
+    :param out_dir: output directory
+    :param pattern of the data files
+    :param unknown_celltypes: which celltypes to merge into the unknown class
+    """
+
+    num_samples = int(
+        num_samples / 2
+    )  # divide by two so half is sparse and half is normal samples
+
+    # List available datasets
+    files = glob.glob(data_path + pattern)
+    files = [os.path.basename(x) for x in files]
+    datasets = [x.split("_")[0] for x in files]
+    print("Datasets: " + str(datasets))
+
+    # Load datasets
+    xs, ys = [], []
+    for i, n in enumerate(datasets):
+        x, y = load_dataset(n, data_path, pattern=pattern)
+        xs.append(x)
+        ys.append(y)
+
+    # Get common gene list
+    all_genes = get_common_genes(xs, type="intersection")
+    print("No. of common genes: " + str(len(all_genes)))
+    xs = [filter_matrix_signature(m, all_genes) for m in xs]
+
+    # Merge unknown celltypes
+    print("Merging unknown cell types: " + str(unknown_celltypes))
+    for i in range(len(ys)):
+        ys[i] = merge_unkown_celltypes(ys[i], unknown_celltypes)
+
+    # Collect all available celltypes
+    celltypes = collect_celltypes(ys)
+    print("Available celltypes: " + str(celltypes))
+    pd.DataFrame(celltypes).to_csv(out_dir + "celltypes.txt", sep="\t")
+
+    # Create signature matrices (for use with Cibersort)
+    sig_mats = []
+    for i in range(len(xs)):
+        sm = generate_signature(xs[i], ys[i])
+        sig_mats.append(sm)
+
+    # Create datasets
+    for i in range(len(xs)):
+        print("Subsampling " + datasets[i] + "...")
+        tmpx, tmpy = create_subsample_dataset(
+            xs[i], ys[i], sample_size, celltypes, num_samples
+        )
+        tmpx.to_csv(out_dir + datasets[i] + "_samples.txt", sep="\t", index=False)
+        tmpy.to_csv(out_dir + datasets[i] + "_labels.txt", sep="\t", index=False)
+        gc.collect()
+
+    print("Finished!")
diff --git a/scaden/preprocessing/create_h5ad_file.py b/scaden/preprocessing/create_h5ad_file.py
index e54f0e6..4af115f 100644
--- a/scaden/preprocessing/create_h5ad_file.py
+++ b/scaden/preprocessing/create_h5ad_file.py
@@ -12,10 +12,6 @@
 import pandas as pd
 import numpy as np
 
-"""
-Functions
-"""
-
 def parse_data(x_path, y_path):
     """
     Parse data and labels and divide them into training and testset
@@ -37,6 +33,7 @@ def parse_data(x_path, y_path):
 
     return x, y, labels
 
+
 def load_celltypes(brain_training_dir):
 
     celltypes_path = os.path.join(brain_training_dir, "celltypes.txt")
@@ -44,6 +41,7 @@ def load_celltypes(brain_training_dir):
     celltypes = list(celltypes.iloc[:, 1])
     return celltypes
 
+
 def sort_celltypes(ratios, labels, ref_labels):
     """
     Bring ratios in correct order of cell types
@@ -56,73 +54,61 @@ def sort_celltypes(ratios, labels, ref_labels):
     ratios = ratios[:, idx]
     return ratios
 
-"""
-Main Section
-"""
 
-# Argument parsing
-parser = argparse.ArgumentParser()
-parser.add_argument("--data", type=str, help="Directory containg the datsets",
-                    default="/home/kevin/deepcell_project/datasets/PBMCs/training/pbmc_top100_3000_400/")
-parser.add_argument("--out", type=str, help="Output path and name. Must end with h5ad", default="dataset.h5ad")
-parser.add_argument("--pattern", type=str, help="Pattern to use for file collection (default: *_samples.txt", default="*_samples.txt")
-parser.add_argument("--unknown", type=str, help="Cells to mark as unknown in the h5ad file. Can be used for gouping.",
-                    default=["Unknown"])
-args = parser.parse_args()
-
-data_dir = args.data
-out_path = args.out
-pattern = args.pattern
-unknown = args.unknown
-
-# List available datasets
-files = glob.glob(data_dir + pattern)
-files = [os.path.basename(x) for x in files]
-datasets = [x.split("_")[0] for x in files]
-
-# get celltypes
-celltypes = load_celltypes(data_dir)
-print("Celltypes: " + str(celltypes))
-
-adata = []
-me_dict = {}
-
-# Create adata datasets for each
-for i, train_file in enumerate(datasets):
-
-    rna_file = os.path.join(data_dir, train_file + "_samples.txt")
-    ratios_file = os.path.join(data_dir, train_file + "_labels.txt")
-
-    x, y, labels = parse_data(rna_file, ratios_file)
-    # sort y
-    y = sort_celltypes(y, labels, celltypes)
-    test = [labels.index(x) for x in celltypes]
-    labels = [labels[i] for i in test]
-
-    x = x.sort_index(axis=1)
-    ratios = pd.DataFrame(y, columns=celltypes)
-    ratios['ds'] = pd.Series(np.repeat(train_file, y.shape[0]),
-                             index=ratios.index)
-
-
-    print("Processing " + str(train_file))
-    x = pd.DataFrame(x)
-    adata.append(anndata.AnnData(X=x.to_numpy(),
-                                 obs=ratios,
-                                 var=pd.DataFrame(columns=[], index=list(x))))
-import gc
-for i in range(1, len(adata)):
-    print("Concatenating " + str(i))
-    adata[0] = adata[0].concatenate(adata[1])
-    del adata[1]
-    gc.collect()
-    print(len(adata))
-adata = adata[0]
-
-
-# add cell types and signature genes
-adata.uns['cell_types'] = celltypes
-adata.uns['unknown'] = unknown
-
-# save data
-adata.write(out_path)
+def create_h5ad_file(data_dir, out_path, unknown, pattern="*_samples.txt"):
+    """
+    Create h5ad file from simulated data
+    """
+
+    # List available datasets
+    files = glob.glob(data_dir + pattern)
+    files = [os.path.basename(x) for x in files]
+    datasets = [x.split("_")[0] for x in files]
+
+    # get celltypes
+    celltypes = load_celltypes(data_dir)
+    print(f"Celltypes: {celltypes}")
+    print(f"Found datasets: {datasets}")
+    adata = []
+    me_dict = {}
+
+    # Create adata datasets for each
+    for i, train_file in enumerate(datasets):
+
+        rna_file = os.path.join(data_dir, train_file + "_samples.txt")
+        ratios_file = os.path.join(data_dir, train_file + "_labels.txt")
+
+        x, y, labels = parse_data(rna_file, ratios_file)
+
+        # sort y
+        y = sort_celltypes(y, labels, celltypes)
+        test = [labels.index(x) for x in celltypes]
+        labels = [labels[i] for i in test]
+
+        x = x.sort_index(axis=1)
+        ratios = pd.DataFrame(y, columns=celltypes)
+        ratios["ds"] = pd.Series(np.repeat(train_file, y.shape[0]), index=ratios.index)
+
+        print("Processing " + str(train_file))
+        x = pd.DataFrame(x)
+        adata.append(
+            anndata.AnnData(
+                X=x.to_numpy(), obs=ratios, var=pd.DataFrame(columns=[], index=list(x))
+            )
+        )
+    import gc
+
+    for i in range(1, len(adata)):
+        print("Concatenating " + str(i))
+        adata[0] = adata[0].concatenate(adata[1])
+        del adata[1]
+        gc.collect()
+        print(len(adata))
+    adata = adata[0]
+
+    # add cell types and signature genes
+    adata.uns["cell_types"] = celltypes
+    adata.uns["unknown"] = unknown
+
+    # save data
+    adata.write(out_path)
diff --git a/scaden/preprocessing/simulate.py b/scaden/preprocessing/simulate.py
new file mode 100644
index 0000000..5a15cc0
--- /dev/null
+++ b/scaden/preprocessing/simulate.py
@@ -0,0 +1,27 @@
+from scaden.preprocessing.create_h5ad_file import create_h5ad_file
+from scaden.preprocessing.bulk_simulation import simulate_bulk
+import os
+"""
+Simulation of artificial bulk RNA-seq samples from scRNA-seq data
+and subsequenbt formatting in .h5ad file for training with Scaden
+"""
+
+def simulation(simulate_dir, data_dir, sample_size, num_samples, pattern, unknown_celltypes, out_prefix):
+
+    # Simulate the data
+    simulate_bulk(
+        sample_size, 
+        num_samples, 
+        data_dir, 
+        simulate_dir, 
+        pattern, 
+        unknown_celltypes
+        )
+
+    # Create the h5ad training data file
+    out_name = os.path.join(simulate_dir, out_prefix + ".h5ad")
+    create_h5ad_file(
+        simulate_dir, 
+        out_name, 
+        unknown_celltypes
+        )

From 75b87b58a24d5107385043accda9b8bd75f44b25 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 09:35:02 +0100
Subject: [PATCH 4/9] fixed bug with parsing unknown cell types

---
 scaden/__main__.py               | 7 ++++---
 scaden/preprocessing/simulate.py | 3 ++-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/scaden/__main__.py b/scaden/__main__.py
index b25b356..f483f84 100644
--- a/scaden/__main__.py
+++ b/scaden/__main__.py
@@ -178,9 +178,10 @@ def process(data_path, prediction_data, processed_path, var_cutoff):
     help = "File pattern to recognize your processed scRNA-seq count files"
 )
 @click.option(
-    '--unknown', '-m',
-    default = ['unkown'],
-    help = "Specifiy cell types to merge into the unknown category."
+    '--unknown', '-u',
+    multiple = True,
+    default = ['unknown'],
+    help = "Specifiy cell types to merge into the unknown category. Specify this flag for every cell type you want to merge in unknown. [default: unknown]"
 
 )
 @click.option(
diff --git a/scaden/preprocessing/simulate.py b/scaden/preprocessing/simulate.py
index 5a15cc0..21c824a 100644
--- a/scaden/preprocessing/simulate.py
+++ b/scaden/preprocessing/simulate.py
@@ -8,7 +8,8 @@
 
 def simulation(simulate_dir, data_dir, sample_size, num_samples, pattern, unknown_celltypes, out_prefix):
 
-    # Simulate the data
+    # Perform the bulk simulation
+    unknown_celltypes = list(unknown_celltypes)
     simulate_bulk(
         sample_size, 
         num_samples, 

From b52d44bb943addc5b1f37d5f9c601728147c4386 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 09:46:29 +0100
Subject: [PATCH 5/9] updated changelog and docs

---
 CHANGELOG.md  |  1 +
 docs/index.md | 23 ++++++++++++++++++++---
 docs/usage.md | 29 +++++++++--------------------
 3 files changed, 30 insertions(+), 23 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bc2d954..c7ed661 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## v0.9.5
 
+* added `scaden simulate` command to perform bulk simulation and training file creation
 * changed CLI calling
 
 ## v0.9.4
diff --git a/docs/index.md b/docs/index.md
index 9eb4014..4a8ea6c 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -10,14 +10,31 @@ A pre-print describing the method is available on Biorxiv:
 [Deep-learning-based cell composition analysis from tissue expression profiles](https://www.biorxiv.org/content/10.1101/659227v1)
 
 
-## Version 0.9.1
-Changelog:
+
+
+
+## Changelog
+
+### Version 0.9.5
++ added `scaden simulate` command to perform bulk simulation and training file creation
+
+### Version 0.9.4
++ fixed dependencies (added python>=3.6 requirement)
+
+### Version 0.9.3
++ upgrade to Tensorflow 2
++ cleaned up dependencies
+
+### Version 0.9.2
++ RAM usage improvement
+
+### Version 0.9.1
 + Added automatic removal of duplicate genes in Mixture file 
 + Changed name of final prediction file
 + Added Scaden logo to main script
 
 
-## Version 0.9.0
+### Version 0.9.0
 This is the initial release version of Scaden. While this version contains full functionality for pre-processing, training and prediction, it does not
 contain thorough error messages, plotting functionality and a solid helper function for generation training data. These are all features
 planned for the release of v.1.0.0.
diff --git a/docs/usage.md b/docs/usage.md
index 80d699a..ab71666 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -88,15 +88,9 @@ Your data can either be raw counts or normalized, just make sure that they are n
 So as long as they are not already in logarithmic space, Scaden will be able to handle both raw and normalized counts / expression values.
 
 ## Training data generation
-#### Under Development 
-As version 0.9.2 is a pre-release version of Scaden, generation of artificial bulk RNA-seq data is not nicely implemented yet, but Scaden still ships with all the scripts to do it. 
-There are generally three steps you have to do to generate training data, given you have a suitable scRNA-seq dataset:
 
-* Generate normalized counts and associated cell type labels
-* Generate artificial bulk samples
-* Merge all samples into a h5ad file
-
-I'll quickly explain how to go about that currently. I plan to make this workflow much easier in the future.
+To generate training data for Scaden, you will first have to process the scRNA-seq dataset(s) you want to use for training.
+Once you have done this, you can use Scaden's command `scaden simulate` to generate the actual training data. I will explain the process in the following.
 
 #### scRNA-seq data processing
 The first step is to process your scRNA-seq dataset(s) you want to use for training. I used Scanpy for this, and would therefore
@@ -108,26 +102,21 @@ column, which Scaden uses to extract the information. The count data should be o
 The order must be the same as for the cell type labels.
 
 #### Bulk simulation
-Once the data is processed, you can use the script 'bulk_simulation.py' provided with Scaden (preprocessing subdirectory) to generate your artificial samples.
-Currently, for Scaden to properly load a dataset for simulation (or several datasets), it must be formatted like this:
+Once the data is processed, you can use the command `scaden simulate` to generate your artificial bulk samples for training.
+To allow Scaden to find your datasets and use them for simulation, they should be stored in the same directory and must be formatted like this:
 
-<dataset_name>_norm_counts_all.txt for the count data
+<dataset_name>_<pattern>.txt for the count data
 
 <dataset_name>_celltypes.txt for the cell type labels 
 
-In future iterations, you will probably have to specify the files directly - which avoids having to used specified file name patterns.
+Here, the `pattern` should be same among all the different datasets (unless you only want to use a specific dataset). 
+
 As example, you can generate 1000 artificial bulk samples from 100 cells per samples with the following command:
 ```console
-python bulk_simulation.py --cells 100 --samples 1000 --data <data_directory> 
+scaden simulate --cells 100 --n_samples 1000 --data <data_directory> --pattern <your_pattern>
 ```
-This would create artificial samples in the current working directory.
 
+This command will create the artificial samples in the current working directory. You can also specificy an output directory using the `--out` parameter. Scaden will also directly create a .h5ad file in this directory, which is the file you will need for training. By default, this file will be called `data.h5ad`, however you can change the prefix using the `--prefix` flag.
 
-#### Create h5ad File
-As final step, you just have to combine your artificial samples in a h5ad file. The 'create_h5ad_file.py' script can be used for this.
-Here's an example:
-```console
-python create_h5ad_file.py --data <directory_with_artificial_samples> --out <name>.h5ad
-```
 
 If you get any errors with the above process, pleas don't hesitate to open an issue on GitHub.
\ No newline at end of file

From 7260af07aa761e481b3e7183a3374da9cfc4363d Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 10:05:20 +0100
Subject: [PATCH 6/9] added seeds for reproducibility

---
 scaden/__main__.py          | 20 ++++++++++++++++----
 scaden/model/scaden.py      |  7 ++++++-
 scaden/scaden/prediction.py | 11 +++++++----
 scaden/scaden/training.py   | 11 +++++++----
 4 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/scaden/__main__.py b/scaden/__main__.py
index f483f84..6c5a457 100644
--- a/scaden/__main__.py
+++ b/scaden/__main__.py
@@ -75,14 +75,20 @@ def cli():
     default = 5000,
     help = 'Number of training steps'
 )
-def train(data_path, train_datasets, model_dir, batch_size, learning_rate, steps):
+@click.option(
+    '--seed',
+    default = 0,
+    help = "Set random seed"
+)
+def train(data_path, train_datasets, model_dir, batch_size, learning_rate, steps, seed):
     """ Train a Scaden model """
     training(data_path=data_path,
                       train_datasets=train_datasets,
                       model_dir=model_dir,
                       batch_size=batch_size,
                       learning_rate=learning_rate,
-                      num_steps=steps)
+                      num_steps=steps,
+                      seed=seed)
 
 
 """
@@ -105,11 +111,17 @@ def train(data_path, train_datasets, model_dir, batch_size, learning_rate, steps
     default = "scaden_predictions.txt",
     help = 'Name of predictions file.'
 )
-def predict(data_path, model_dir, outname):
+@click.option(
+    '--seed',
+    default = 0,
+    help = "Set random seed"
+)
+def predict(data_path, model_dir, outname, seed):
     """ Predict cell type composition using a trained Scaden model"""
     prediction(model_dir=model_dir,
                         data_path=data_path,
-                        out_name=outname)
+                        out_name=outname,
+                        seed=seed)
 
 
 
diff --git a/scaden/model/scaden.py b/scaden/model/scaden.py
index 8cd8f6a..ab252a8 100644
--- a/scaden/model/scaden.py
+++ b/scaden/model/scaden.py
@@ -15,7 +15,7 @@ class Scaden(object):
     scaden class
     """
 
-    def __init__(self, sess, model_dir, model_name, batch_size=128, learning_rate=0.0001,  num_steps=1000):
+    def __init__(self, sess, model_dir, model_name, batch_size=128, learning_rate=0.0001,  num_steps=1000, seed=0):
         self.sess=sess
         self.model_dir=model_dir
         self.batch_size=batch_size
@@ -35,6 +35,11 @@ def __init__(self, sess, model_dir, model_name, batch_size=128, learning_rate=0.
         self.hidden_units = [256, 128, 64, 32]
         self.do_rates = [0, 0, 0, 0]
 
+        # Set seeds for reproducibility
+        tf.random.set_seed(seed)
+        os.environ['TF_DETERMINISTIC_OPS'] = '1'
+        np.random.seed(seed)
+
 
     def model_fn(self, X, n_classes, reuse=False):
         """
diff --git a/scaden/scaden/prediction.py b/scaden/scaden/prediction.py
index 01defd2..8dc33e5 100644
--- a/scaden/scaden/prediction.py
+++ b/scaden/scaden/prediction.py
@@ -31,7 +31,7 @@
 # ==========================================#
 
 
-def prediction(model_dir, data_path, out_name):
+def prediction(model_dir, data_path, out_name, seed=0):
     """
     Perform prediction using a trained scaden ensemble
     :param model_dir: the directory containing the models
@@ -45,7 +45,8 @@ def prediction(model_dir, data_path, out_name):
     with tf.compat.v1.Session() as sess:
         cdn256 = Scaden(sess=sess,
                      model_dir=model_dir + "/m256",
-                     model_name='m256')
+                     model_name='m256',
+                     seed=seed)
         cdn256.hidden_units = M256_HIDDEN_UNITS
         cdn256.do_rates = M256_DO_RATES
 
@@ -58,7 +59,8 @@ def prediction(model_dir, data_path, out_name):
     with tf.compat.v1.Session() as sess:
         cdn512 = Scaden(sess=sess,
                      model_dir=model_dir+"/m512",
-                     model_name='m512')
+                     model_name='m512',
+                     seed=seed)
         cdn512.hidden_units = M512_HIDDEN_UNITS
         cdn512.do_rates = M512_DO_RATES
 
@@ -70,7 +72,8 @@ def prediction(model_dir, data_path, out_name):
     with tf.compat.v1.Session() as sess:
         cdn1024 = Scaden(sess=sess,
                       model_dir=model_dir+"/m1024",
-                      model_name='m1024')
+                      model_name='m1024',
+                      seed=seed)
         cdn1024.hidden_units = M1024_HIDDEN_UNITS
         cdn1024.do_rates = M1024_DO_RATES
 
diff --git a/scaden/scaden/training.py b/scaden/scaden/training.py
index 538863b..f6b04a8 100644
--- a/scaden/scaden/training.py
+++ b/scaden/scaden/training.py
@@ -30,7 +30,7 @@
 # ==========================================#
 
 
-def training(data_path, train_datasets, model_dir, batch_size, learning_rate, num_steps):
+def training(data_path, train_datasets, model_dir, batch_size, learning_rate, num_steps, seed=0):
     """
     Perform training of three a scaden model ensemble consisting of three different models
     :param model_dir:
@@ -56,7 +56,8 @@ def training(data_path, train_datasets, model_dir, batch_size, learning_rate, nu
                      model_name='m256',
                      batch_size=batch_size,
                      learning_rate=learning_rate,
-                     num_steps=num_steps)
+                     num_steps=num_steps,
+                     seed=seed)
         cdn256.hidden_units = M256_HIDDEN_UNITS
         cdn256.do_rates = M256_DO_RATES
         cdn256.train(input_path=data_path, train_datasets=train_datasets)
@@ -71,7 +72,8 @@ def training(data_path, train_datasets, model_dir, batch_size, learning_rate, nu
                      model_name='m512',
                      batch_size=batch_size,
                      learning_rate=learning_rate,
-                     num_steps=num_steps)
+                     num_steps=num_steps,
+                     seed=seed)
         cdn512.hidden_units = M512_HIDDEN_UNITS
         cdn512.do_rates = M512_DO_RATES
         cdn512.train(input_path=data_path, train_datasets=train_datasets)
@@ -86,7 +88,8 @@ def training(data_path, train_datasets, model_dir, batch_size, learning_rate, nu
                       model_name='m1024',
                       batch_size=batch_size,
                       learning_rate=learning_rate,
-                      num_steps=num_steps)
+                      num_steps=num_steps,
+                      seed=seed)
         cdn1024.hidden_units = M1024_HIDDEN_UNITS
         cdn1024.do_rates = M1024_DO_RATES
         cdn1024.train(input_path=data_path, train_datasets=train_datasets)

From 344d4b2eff36bc44a855e6b28b241a0dea2f6a40 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 10:14:35 +0100
Subject: [PATCH 7/9] reduced tensorflow logging

---
 CHANGELOG.md       | 1 +
 docs/index.md      | 1 +
 scaden/__main__.py | 3 +++
 3 files changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c7ed661..752aba2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## v0.9.5
 
+* added `--seed` parameter to allow reproducible Scaden runs
 * added `scaden simulate` command to perform bulk simulation and training file creation
 * changed CLI calling
 
diff --git a/docs/index.md b/docs/index.md
index 4a8ea6c..be88f3c 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -17,6 +17,7 @@ A pre-print describing the method is available on Biorxiv:
 
 ### Version 0.9.5
 + added `scaden simulate` command to perform bulk simulation and training file creation
++ added `--seed` parameter to allow reproducible Scaden runs
 
 ### Version 0.9.4
 + fixed dependencies (added python>=3.6 requirement)
diff --git a/scaden/__main__.py b/scaden/__main__.py
index 6c5a457..9bf5fee 100644
--- a/scaden/__main__.py
+++ b/scaden/__main__.py
@@ -1,5 +1,7 @@
 import click
 import scaden
+import logging
+import os
 from scaden.scaden.training import training
 from scaden.scaden.prediction import prediction
 from scaden.scaden.processing import processing
@@ -11,6 +13,7 @@
 This is the main file for executing the Scaden program.
 """
 
+os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' 
 
 
 def main():

From 9f76232bf202b72fd568564319bc5a387ab54721 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 11:02:20 +0100
Subject: [PATCH 8/9] improved logging of errors

---
 .gitignore                               |  4 ++-
 .vscode/settings.json                    |  5 +++-
 scaden/__main__.py                       |  2 ++
 scaden/preprocessing/bulk_simulation.py  | 37 +++++++++++++++---------
 scaden/preprocessing/create_h5ad_file.py | 20 +++++++++----
 scaden/scaden/training.py                |  2 +-
 6 files changed, 47 insertions(+), 23 deletions(-)

diff --git a/.gitignore b/.gitignore
index eda44ab..fe1a8ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -125,4 +125,6 @@ dmypy.json
 
 # extra
 .idea
-scaden.egg-info
\ No newline at end of file
+scaden.egg-info
+.vscode
+.vscode/
\ No newline at end of file
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 79b73ce..338af49 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,3 +1,6 @@
 {
-    "python.pythonPath": "/home/kevin/anaconda3/envs/scaden/bin/python"
+    "python.pythonPath": "/home/kevin/anaconda3/envs/scaden/bin/python",
+    "python.linting.pylintEnabled": false,
+    "python.linting.enabled": true,
+    "python.linting.flake8Enabled": true
 }
\ No newline at end of file
diff --git a/scaden/__main__.py b/scaden/__main__.py
index 9bf5fee..dd56871 100644
--- a/scaden/__main__.py
+++ b/scaden/__main__.py
@@ -13,6 +13,8 @@
 This is the main file for executing the Scaden program.
 """
 
+# Logging
+logger = logging.getLogger()
 os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' 
 
 
diff --git a/scaden/preprocessing/bulk_simulation.py b/scaden/preprocessing/bulk_simulation.py
index c1d20f6..3db2d3c 100644
--- a/scaden/preprocessing/bulk_simulation.py
+++ b/scaden/preprocessing/bulk_simulation.py
@@ -1,15 +1,16 @@
 #########################################################################
 ## Simulation of artificial bulk RNA-seq datasets from scRNA-seq data   #
 ########################################################################
-
-import pandas as pd
-import numpy as np
-import glob
+import logging
+import sys
 import os
-import argparse
 import gc
+import glob
+import pandas as pd
+import numpy as np
 from tqdm import tqdm
 
+logger = logging.getLogger(__name__)
 
 def create_fractions(no_celltypes):
     """
@@ -170,8 +171,15 @@ def load_dataset(name, dir, pattern):
     """
     pattern = pattern.replace("*", "")
     print("Loading " + name + " dataset ...")
+
+    try:
+        y = pd.read_table(dir + name + "_celltypes.txt")
+    except FileNotFoundError as e:
+        logger.error(f"No celltypes file found for {name}. It should be called {name}_celltypes.txt.")
+        sys.exit()
+
     x = pd.read_table(dir + name + pattern, index_col=0)
-    y = pd.read_table(dir + name + "_celltypes.txt")
+    
     return (x, y)
 
 
@@ -224,10 +232,12 @@ def get_common_genes(xs, type="intersection"):
             com_genes = com_genes.intersection(genes[gi])
 
     else:
-        exit("Wrong type selected to get common genes. Exiting.")
+        logging.critical("Wrong type selected to get common genes. Exiting.")
+        sys.exit()
 
     if len(com_genes) == 0:
-        exit("No common genes found. Exiting.")
+        logging.critical("No common genes found. Exiting.")
+        sys.exit()
 
     return list(com_genes)
 
@@ -273,6 +283,11 @@ def simulate_bulk(
     files = glob.glob(data_path + pattern)
     files = [os.path.basename(x) for x in files]
     datasets = [x.split("_")[0] for x in files]
+
+    if len(datasets) == 0:
+        logging.error("No datasetes fround! Have you specified the pattern correctly?")
+        sys.exit()
+
     print("Datasets: " + str(datasets))
 
     # Load datasets
@@ -297,12 +312,6 @@ def simulate_bulk(
     print("Available celltypes: " + str(celltypes))
     pd.DataFrame(celltypes).to_csv(out_dir + "celltypes.txt", sep="\t")
 
-    # Create signature matrices (for use with Cibersort)
-    sig_mats = []
-    for i in range(len(xs)):
-        sm = generate_signature(xs[i], ys[i])
-        sig_mats.append(sm)
-
     # Create datasets
     for i in range(len(xs)):
         print("Subsampling " + datasets[i] + "...")
diff --git a/scaden/preprocessing/create_h5ad_file.py b/scaden/preprocessing/create_h5ad_file.py
index 4af115f..3ef423b 100644
--- a/scaden/preprocessing/create_h5ad_file.py
+++ b/scaden/preprocessing/create_h5ad_file.py
@@ -4,14 +4,17 @@
 
 When using additional datasets, they should be in similar format and best have the same output cell types.
 """
-
-import argparse
+import gc
 import anndata
 import glob
 import os
+import sys
+import logging
 import pandas as pd
 import numpy as np
 
+logger = logging.getLogger(__name__)
+
 def parse_data(x_path, y_path):
     """
     Parse data and labels and divide them into training and testset
@@ -20,8 +23,12 @@ def parse_data(x_path, y_path):
     :return: training and test data and labels
     """
     # Load the data
-    x = pd.read_table(x_path, sep="\t")
-    y = pd.read_table(y_path, sep="\t")
+    try:
+        x = pd.read_table(x_path, sep="\t")
+        y = pd.read_table(y_path, sep="\t")
+    except FileNotFoundError as e:
+        logging.error(f"Could not find simulated data files: {e}")
+        sys.exit()
     labels = list(y.columns)
 
     # Transform Y to numpy array and split in train and testset
@@ -96,8 +103,9 @@ def create_h5ad_file(data_dir, out_path, unknown, pattern="*_samples.txt"):
                 X=x.to_numpy(), obs=ratios, var=pd.DataFrame(columns=[], index=list(x))
             )
         )
-    import gc
-
+        
+        
+    
     for i in range(1, len(adata)):
         print("Concatenating " + str(i))
         adata[0] = adata[0].concatenate(adata[1])
diff --git a/scaden/scaden/training.py b/scaden/scaden/training.py
index f6b04a8..3d84157 100644
--- a/scaden/scaden/training.py
+++ b/scaden/scaden/training.py
@@ -44,7 +44,7 @@ def training(data_path, train_datasets, model_dir, batch_size, learning_rate, nu
         train_datasets = []
     else:
         train_datasets = train_datasets.split()
-    print("Training on: " + str(train_datasets))
+        print(f"Training on: {train_datasets}")
 
 
     # M256 model training

From 703458ce5c2d4ab83c11e81d2099c44a7e203fe1 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Sun, 13 Dec 2020 11:15:11 +0100
Subject: [PATCH 9/9] version 0.9.5

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index cb06aa8..03cd660 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = '0.9.4'
+version = '0.9.5'
 
 
 with open("README.md", "r", encoding="UTF-8") as fh: