DESCRIPTION

Package: chipenrich
Type: Package
Title: Gene Set Enrichment For ChIP-seq Peak Data
Version: 2.23.1
Date: 2023-03-29
Authors@R: c(
	person(c("Ryan","P."),"Welch",role = c("aut","cph"),email = "welchr@umich.edu"),
	person("Chee","Lee",role = c("aut"),email = "cheelee@umich.edu"),
	person(c("Raymond","G."),"Cavalcante",role = c("aut"),email = "rcavalca@umich.edu"),
	person("Kai","Wang",role = c("cre"),email = "wangdaha@umich.edu"),
	person("Chris","Lee",role = c("aut"),email = "leetaiyi@umich.edu"),
	person(c("Laura","J."),"Scott",role = c("ths"), email = "ljst@umich.edu"),
	person(c("Maureen","A."),"Sartor",role = c("ths"),email = "sartorma@med.umich.edu"))
Description: ChIP-Enrich and Poly-Enrich perform gene set enrichment testing
	using peaks called from a ChIP-seq experiment. The method empirically
	corrects for confounding factors such as the length of genes,
	and the mappability of the sequence surrounding genes.
biocViews: ImmunoOncology, ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression
License: GPL-3
Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb,
        GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra,
        MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db,
        org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer,
        S4Vectors (>= 0.23.10), stats, stringr, utils
Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
Depends: R (>= 3.4.0)
LazyLoad: yes
Maintainer: Kai Wang <wangdaha@umich.edu>
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Collate:
	'assign_peaks.R'
	'test_broadenrich.R'
	'peaks_per_gene.R'
	'read.R'
	'randomize.R'
	'setup.R'
	'supported.R'
	'utils.R'
	'constants.R'
	'plot_gene_coverage.R'
	'broadenrich.R'
	'test_chipapprox.R'
	'test_chipenrich.R'
	'test_chipenrich_slow.R'
	'test_fisher.R'
	'test_binomial.R'
	'test_approx.R'
	'plot_chipenrich_spline.R'
	'plot_dist_to_tss.R'
	'chipenrich.R'
	'chipenrich_package_doc.R'
	'test_polyapprox.R'
	'test_polyenrich_weighted.R'
	'test_polyenrich_slow.R'
	'test_polyenrich.R'
	'plot_polyenrich_spline.R'
	'polyenrich.R'
	'hybrid.R'
	'peak_weights.R'
	'peaks2genes.R'
	'test_proxReg.R'
	'proxReg.R'