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ShinyArchR_testPull#1799

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rcorces wants to merge 175 commits intoGreenleafLab:devGreenleafLab/ArchR:devfrom paupaiz:devpaupaiz/ArchR:devCopy head branch name to clipboard

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Commits

Commits on Oct 20, 2022

• integrating ShinyArchR to main codebase

  paupaiz

  committed
  14e2c00

Commits on Nov 1, 2022

• Merge branch 'GreenleafLab:dev' into dev

  paupaiz

  authored
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Commits on Nov 3, 2022

• Merge branch 'GreenleafLab:dev' into dev

  paupaiz

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• modifying after deploying

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Commits on Nov 7, 2022

• add a @param definition for Shiny loadArchRproj()

  paupaiz

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  a25b9fc

• Update AnnotationGenome.R

  paupaiz

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• Merge branch 'GreenleafLab:dev' into dev

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  5844720

• Update ArchRBrowser.R

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  a0ca2d4

• adding .validInput to shinyarchr

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  3ee4410

• pattern match to list coverage files

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  93a5fd9

• use previously stored cellGroups

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  4495ed8

Commits on Nov 14, 2022

• Merge branch 'GreenleafLab:dev' into dev

  paupaiz

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  5e0c9e4

• force create coverage

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  paupaiz

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  68ea6b0

• safelapply to .getGroupFragsFromProj

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  paupaiz

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  3a62d51

• cellGroups for consistency

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  e281685

• change cluster to groupIDs

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  25f39b5

• fragFiles

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  455724f

• fix the path to the ArchRProject outputDirectory

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  c748edf

• correct gsub

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  9e7f165

• modify to ShinyRasterUMAPs

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Commits on Nov 15, 2022

• removing most ArchR::: mine

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• remove ArchR::: to load hidden functions

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Commits on Nov 17, 2022

• downloadFiles()

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• removing all the ArchR:::

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• adding all files with ArchR:::

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  09eb384

• saving ArchRProjShiny

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• adding arguments to exportShinyArchR

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Commits on Nov 18, 2022

• allow for any embedding in mainUMAPs WIP

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Commits on Nov 27, 2022

• Merge branch 'GreenleafLab:dev' into dev

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• "de-hard-coding embeddings"

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• de-hardcoding embeds

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Commits on Dec 4, 2022

• multiple changes have been made

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  paupaiz

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  77e49db

• Hardcodings and duplicated part removed

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• Minor changes have been made.

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Commits on Dec 5, 2022

• Merge branch 'GreenleafLab:dev' into dev

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  d57a3b0

Commits on Dec 9, 2022

• Delete plotEmbeddingShiny, added new arguments.

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• getFeatureDF

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Commits on Dec 11, 2022

• fixing minor issues

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• fixed the reported issues

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  a067832

• fixed the reported issues

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• fixed the reported issues

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Commits on Dec 12, 2022

• Merge branch 'GreenleafLab:dev' into dev

  paupaiz

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• cleaning up

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Commits on Dec 19, 2022

• Hardcodings are removed. Available matrices are used

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  c2dea08

• Hardcodings are removed. Available matrices used.

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  48834a5

• Minor bug fixed.

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  4fd11f0

• remove unnecessary lines

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  2d51d61

• availableArrays(head(getArrowFiles(ArchRProj), 2)

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  80ef7cd

• changed umap to embed

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  ca186d6

• change umap to embed

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  e7e394d

• change umap to embed

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Commits on Dec 29, 2022

• minor fixes

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  ce79920

• minor fixes

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  bacc77e

• major improvements

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  5ff434d

• Update and rename shinyRasterUMAPs to matrixEmbeds

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Commits on Dec 30, 2022

• Merge remote-tracking branch 'remotes/upstream/dev' into tmp

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Commits on Jan 3, 2023

• shiny files

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  17d36da

• remove duplicate myloadarchrproj

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  5b6d19b

• moving shiny files to shiny dir

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  80e8ed0

Commits on Jan 5, 2023

• fixed a minor issue

  paupaiz

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  f5110b8

• update shiny variable name and desc

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  93a8a7e

• fix incorrect conflict resolution

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  4b58f44

• bugfix in example

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  0ff7fd5

• change default outDir

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  rcorces

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  88c2be1

• fix fragDir and frag file extension

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  rcorces

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  9499c5b

Commits on Jan 11, 2023

• Merge branch 'GreenleafLab:dev' into dev

  paupaiz

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  6219bb7

• cleaning up

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  6132875

Commits on Jan 12, 2023

• clean up

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  1f9e56a

• changing imputeMatricesList to imputMatrices

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  d7749b9

• merging plotEmbedding

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  67eee17

• exportShinyArchR

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  3d283c5

• exportShinyArchR

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  74a1492

Commits on Jan 13, 2023

• update plotembedding for shiny

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  e50904e

• update plotembedding

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  c3cd3b8

Commits on Jan 14, 2023

• fixing MatrixEmbeds

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  884b86d

Commits on Jan 16, 2023

• Update ArchRBrowser.R

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  rcorces

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  75afaba

Commits on Jan 17, 2023

• tidying code for legibility

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  5b639e4

• change validInput for consistent format

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  4879cd9

• fix dir structure and consolidate shiny functions

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  rcorces

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  d203693

• Delete matrixEmbeds.R

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  f535755

• Delete MainEmbed.R

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  fdd8a33

• Delete .DS_Store

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  437db73

• Delete .DS_Store

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  9c04fe6

• Delete .DS_Store

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  9670243

• Delete .DS_Store

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  291cf0c

• Delete .DS_Store

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  5abf0f1

• Delete .DS_Store

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  de512c7

• Delete .DS_Store

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  c30cc5d

• harmonize mainEmbeds and matrixEmbeds

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  1681eb2

• partial update to exportShinyArchR

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  rcorces

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  99915f2

• additional shiny export edits

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• typos

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Commits on Jan 18, 2023

• revert all changes

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  25eeab3

• revert all changes

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Commits on Jan 21, 2023

• adding matrices list to mainembeds fun

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Commits on Jan 29, 2023

• correcting parentheses in getgroupfrag and cov funs

  

  pauline Paiz

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Commits on Jan 31, 2023

• ahora si

  

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Commits on Feb 4, 2023

• typo computeClosestCellsList

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Commits on Feb 19, 2023

• from pelayo

  

  pauline Paiz

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Commits on Feb 23, 2023

• changing matrixEmbeds variables to be consistent

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• matrixEmbeds updates

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Commits on Feb 26, 2023

• "adding shinyarchr exports to collate field"

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• adding comma to loadArchRProject

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• "typo"

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• ellColEmbeddings parameter

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• end space visualize data

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  b3881e9

• latest global server ui files

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Commits on Feb 28, 2023

• newlines

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Commits on Mar 1, 2023

• getMatrixValues

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• Update AllClasses.R

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• Merge branch 'dev' into dev_mrc2

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  a8b887b

• Merge pull request #3 from paupaiz/dev_mrc2

  Show description for fe7dc4a
  rcorces

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  fe7dc4a

• add NULL

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  b2627c9

• Update GroupExport.R

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  paupaiz

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  6ae5a83

• update function

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  5d41b80

• Update VisualizeData.R

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  bb5484e

• Update ShinyArchRExports.R

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  f9d6bd4

• Update VisualizeData.R

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  8049bfa

• Update ShinyArchRExports.R

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  3f10ff5

• Update ShinyArchRExports.R

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  e478e03

• Update ShinyArchRExports.R

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  4c82e96

• Update ShinyArchRExports.R

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  1c33932

• Update ShinyArchRExports.R

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  c7dc708

• Update ShinyArchRExports.R

  paupaiz

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  a5de624

• Update ShinyArchRExports.R

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  8ab4bab

Commits on Mar 2, 2023

• Update ShinyArchRExports.R

  paupaiz

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  18207fb

• Update ShinyArchRExports.R

  paupaiz

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Commits on Mar 16, 2023

• Add validInput for ShinyArchR

  rcorces

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  8a0a167

• add threads option to getGroupFragsFromProj

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  rcorces

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  1e8a876

• change function name

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  rcorces

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  e9e2698

• change function name

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  rcorces

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  3c1abf1

• fix mainDir path issues

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  rcorces

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  e47e4b1

• update DESCRIPTION to reflect ArchR/dev

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  8383fe3

Commits on Mar 17, 2023

• add explicit package mentions

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  2cfc1f8

• update file download links

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  18fb6c6

• shouldnt need to source if ArchR is loaded

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  8443d6d

• bugfixes

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  2441acf

Commits on Mar 24, 2023

• code review

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  rcorces

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  9b83c0a

• ensure closure of H5s

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  f646a05

• update file md5s. fix h5group creation

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  eac195f

• bugfix

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  a24a4dc

• update example

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  1f8b1f1

Commits on Mar 25, 2023

• hiding addSeqLengths

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  de261e8

• safelapply for explorClusterCvgs

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  2987355

Commits on Mar 27, 2023

• getting units from the ArchRProj (not ArchRProjShiny)

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  84af7ad

• adding stop condition

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  39622f9

• bugfix (file does not exist)

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  rcorces

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  5c27360

• return null instead of last result

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  9351c90

Commits on Mar 28, 2023

• remove Shiny version of plotEmbedding

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  1325172

• bugfix

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  e484d36

• bugfix

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  89fd4af

• add threads argument to exportClusterCoverage

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  d535380

• bugfix addSeqLengths is hidden

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  bbb2c9f

• bugfix old arguments

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  415a8a4

• add back feature name storage

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  0cc7457

• remove explicit namespace loading from global

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  2b1d8fc

• bugfix dir name

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  fc3f673

• typo

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• add status reporting for feature plots

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  e742abb

• pass logFile to plotEmbedding

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  4b37476

• Merge branch 'dev' into dev_mrcPlotEmbedding

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• typo

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  ee7e553

• remove Shiny version of plotEmbedding

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• bugfix

  

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  2b577fb

• bugfix

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  3d43d13

• add threads argument to exportClusterCoverage

  

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  7872f6a

• bugfix addSeqLengths is hidden

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  paupaiz

  committed
  18bdc87

• bugfix old arguments

  

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  0139212

• add back feature name storage

  

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  5d6cb74

• remove explicit namespace loading from global

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  paupaiz

  committed
  2813105

• bugfix dir name

  

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  9ad2026

• typo

  

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  6fb28fd

• add status reporting for feature plots

  

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  4807128

• pass logFile to plotEmbedding

  

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  b6b1287

• Merge pull request #4 from paupaiz/dev_mrcPlotEmbedding

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  paupaiz

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  c970e0e