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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

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Commits on Nov 1, 2022

• Merge branch 'GreenleafLab:dev' into dev

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Commits on Nov 3, 2022

• Merge branch 'GreenleafLab:dev' into dev

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• modifying after deploying

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Commits on Nov 7, 2022

• add a @param definition for Shiny loadArchRproj()

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• Update AnnotationGenome.R

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• Merge branch 'GreenleafLab:dev' into dev

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• Update ArchRBrowser.R

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• adding .validInput to shinyarchr

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• pattern match to list coverage files

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• use previously stored cellGroups

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Commits on Nov 14, 2022

• Merge branch 'GreenleafLab:dev' into dev

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• force create coverage

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• safelapply to .getGroupFragsFromProj

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• cellGroups for consistency

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• change cluster to groupIDs

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• fragFiles

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• fix the path to the ArchRProject outputDirectory

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• correct gsub

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• 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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• 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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• 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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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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• 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

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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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• Hardcodings are removed. Available matrices used.

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• Minor bug fixed.

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• remove unnecessary lines

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

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• changed umap to embed

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• change umap to embed

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• change umap to embed

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Commits on Dec 29, 2022

• minor fixes

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• minor fixes

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• major improvements

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• 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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• remove duplicate myloadarchrproj

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• moving shiny files to shiny dir

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Commits on Jan 5, 2023

• fixed a minor issue

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• update shiny variable name and desc

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• fix incorrect conflict resolution

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• bugfix in example

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• change default outDir

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• fix fragDir and frag file extension

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Commits on Jan 11, 2023

• Merge branch 'GreenleafLab:dev' into dev

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• cleaning up

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Commits on Jan 12, 2023

• clean up

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• changing imputeMatricesList to imputMatrices

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• merging plotEmbedding

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• exportShinyArchR

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• exportShinyArchR

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Commits on Jan 13, 2023

• update plotembedding for shiny

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• update plotembedding

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Commits on Jan 14, 2023

• fixing MatrixEmbeds

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Commits on Jan 16, 2023

• Update ArchRBrowser.R

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Commits on Jan 17, 2023

• tidying code for legibility

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• change validInput for consistent format

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• fix dir structure and consolidate shiny functions

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• Delete matrixEmbeds.R

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• Delete MainEmbed.R

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• Delete .DS_Store

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• Delete .DS_Store

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• Delete .DS_Store

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• Delete .DS_Store

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• Delete .DS_Store

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• Delete .DS_Store

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• Delete .DS_Store

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• harmonize mainEmbeds and matrixEmbeds

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• partial update to exportShinyArchR

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• 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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• 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

  

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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

  

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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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• 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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• Merge pull request #3 from paupaiz/dev_mrc2

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• add NULL

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• Update GroupExport.R

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• update function

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• Update VisualizeData.R

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• Update ShinyArchRExports.R

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• Update VisualizeData.R

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• Update ShinyArchRExports.R

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• Update ShinyArchRExports.R

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• Update ShinyArchRExports.R

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• Update ShinyArchRExports.R

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• Update ShinyArchRExports.R

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• Update ShinyArchRExports.R

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• Update ShinyArchRExports.R

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Commits on Mar 2, 2023

• Update ShinyArchRExports.R

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• Update ShinyArchRExports.R

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Commits on Mar 16, 2023

• Add validInput for ShinyArchR

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• add threads option to getGroupFragsFromProj

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• change function name

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• change function name

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• fix mainDir path issues

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• update DESCRIPTION to reflect ArchR/dev

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Commits on Mar 17, 2023

• add explicit package mentions

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• update file download links

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• shouldnt need to source if ArchR is loaded

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• bugfixes

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Commits on Mar 24, 2023

• code review

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• ensure closure of H5s

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• update file md5s. fix h5group creation

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• bugfix

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• update example

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Commits on Mar 25, 2023

• hiding addSeqLengths

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• safelapply for explorClusterCvgs

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Commits on Mar 27, 2023

• getting units from the ArchRProj (not ArchRProjShiny)

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• adding stop condition

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• bugfix (file does not exist)

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• return null instead of last result

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Commits on Mar 28, 2023

• remove Shiny version of plotEmbedding

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• bugfix

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• bugfix

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• add threads argument to exportClusterCoverage

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• bugfix addSeqLengths is hidden

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• bugfix old arguments

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• add back feature name storage

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• remove explicit namespace loading from global

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• bugfix dir name

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• typo

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• add status reporting for feature plots

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• pass logFile to plotEmbedding

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• Merge branch 'dev' into dev_mrcPlotEmbedding

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• typo

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• remove Shiny version of plotEmbedding

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• bugfix

  

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• bugfix

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• add threads argument to exportClusterCoverage

  

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• bugfix addSeqLengths is hidden

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• bugfix old arguments

  

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• add back feature name storage

  

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• remove explicit namespace loading from global

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• bugfix dir name

  

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• typo

  

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• add status reporting for feature plots

  

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• pass logFile to plotEmbedding

  

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• Merge pull request #4 from paupaiz/dev_mrcPlotEmbedding

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