Files in jn-goe/gruffi

Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md .github/ISSUE_TEMPLATE/question.md FAQ.md Functions.md R/gruffi.R R/gruffi.optional.R README.md dev/Create_the_gruffi_Package.R dev/Create_the_gruffi_Package_OLD.R dev/Dependencies.R dev/Install.Dependencies.Gruffi.R dev/StressUMAP.alt.R dev/config.OLD.R dev/config.R dev/list.of.functions.in.gruffi.det.md dev/realase.md filter.script.example.R inst/shiny/GO.thresh/server.R inst/shiny/GO.thresh/ui.R man/AddCustomScore.Rd man/AddGOGeneList.manual.Rd man/AddGOScore.Rd man/AssignGranuleAverageScoresFromGOterm.Rd man/AutoFindGranuleResolution.Rd man/CalcClusterAverages_Gruffi.Rd man/CalcStandDevSkewedDistr.Rd man/CalcTranscriptomePercentage.Rd man/CalcTranscriptomePercentageGO.Rd man/CalculateAndPlotGoTermScores.Rd man/CalculateMedianClusterSize.Rd man/CleanDuplicateScorenames.Rd man/ClearGruffi.Rd man/ClusterUMAPthresholding.Rd man/CustomScoreEvaluation.Rd man/FeaturePlotSaveCustomScore.Rd man/FeaturePlotSaveGO.Rd man/FilterStressedCells.Rd man/FindThresholdsAuto.Rd man/FindThresholdsShiny.Rd man/GetAllGOTermNames.Rd man/GetGOTerms.Rd man/GetGruffiClusteringName.Rd man/GrScoreHistogram.Rd man/GrScoreUMAP.Rd man/IntersectWithExpressed.Rd man/ParseGruffiGranuleScoreName.Rd man/PlotClustSizeDistr.Rd man/PlotNormAndSkew.Rd man/ReassignSmallClusters.Rd man/StressBarplotPerCluster.Rd man/StressUMAP.Rd man/UMAP3Dcubes.Rd man/dot-convert.GO_term.2.score.Rd man/dot-convert.score.2.GO_term.Rd man/dot-fix.metad.colname.rm.trailing.1.Rd man/dot-parse.GO.Rd man/dot-round.Rd