Files in bimberlabinternal/OOSAP
OHSU-ONPRC Single-cell Analysis Package
.DS_Store
.Rbuildignore
.dockerignore
.github/prepareEnvironment.sh
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yml
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
OOSAP.iml
OOSAP.ipr
R/Classification_Caret.R
R/Classification_Garnett.R
R/Classification_MCE.R
R/Classification_SGS.R
R/Classification_Sim.R
R/GeneAliasing.R
R/GeneNames.R
R/LabKeySettings.R
R/Monocle_III.R
R/PhenotypingGeneSets.R
R/PseudoBulk.R
R/Seurat_III.R
R/SingleR_Seurat.R
R/Utils.R
R/Viz.R
R/data.R
R/mcl.R
R/plotDiffusionMaps.R
R/postSDA_processing.R
R/sysdata.rda
README.md
data/cdGenes.rda
man/AddClonesToPlot.Rd
man/AliasGeneNames.Rd
man/AvgCellExprs.Rd
man/CalculateModuleScoreAvg.Rd
man/CheckDuplicatedCellNames.Rd
man/ClassifySGS.Rd
man/ClassifySGSAndApply.Rd
man/ClassifySGS_Multiple.Rd
man/ColorTheme.Rd
man/CreateSeuratObj.Rd
man/DimPlot_SingleRClassLabs.Rd
man/FilterCloneNames.Rd
man/FindClustersAndDimRedux.Rd
man/FindElbow.Rd
man/FindSeuratElbow.Rd
man/Find_Markers.Rd
man/Garnett_Classification.Rd
man/GetEnsmbleVarImportance.Rd
man/GetGeneIds.Rd
man/GetTraingStats.Rd
man/GetXYDataFromPlot.Rd
man/HasStepRun.Rd
man/LogAdd.Rd
man/MDSmyDF.Rd
man/MarkStepRun.Rd
man/MergeSeuratObjs.Rd
man/MultiClassifier_Cells.Rd
man/PCAmyDF.Rd
man/PerformEmptyDropletFiltering.Rd
man/PerformEmptyDrops.Rd
man/Phenotyping_GeneList.Rd
man/PlotAvgExpr.Rd
man/PlotBin2D.Rd
man/PlotDiffComp.Rd
man/PlotDiffComp2.Rd
man/PlotExprThrTab.Rd
man/PlotFeatThrTab.Rd
man/PlotHistDensOptima.Rd
man/PlotImmuneMarkers.Rd
man/PlotMarkerSeries.Rd
man/PlotMarkerSet.Rd
man/PlotMyTable.Rd
man/PrintQcPlots.Rd
man/ProcessSeurat1.Rd
man/QueryEnsemblSymbolAndHumanHomologs.Rd
man/ReadAndFilter10xData.Rd
man/RecomposeSDAmatrix.Rd
man/RecreateSeuratObjFromSDAmatrix.Rd
man/RemoveCellCycle.Rd
man/RemoveUnchangedOrZero.Rd
man/RunSingleR.Rd
man/RunUMAP.Matrix.Rd
man/SaveDimRedux.Rd
man/Ser2Monicle_MakeNProcess.Rd
man/SetIfNull.Rd
man/Tabulate_SingleRClassLabs.Rd
man/TranslateGeneNames.Rd
man/TranslateToDAVID.Rd
man/TranslateToEnsembl.Rd
man/TranslateToStringDb.Rd
man/TransposeDT.Rd
man/UniformSampleDF_FacPor.Rd
man/WichIn1not2.Rd
man/WriteCellBarcodes.Rd
man/WriteSummaryMetrics.Rd
man/bimodal_posDisHD.Rd
man/bimodal_posDist1D.Rd
man/cdGenes.Rd
man/cells2AvgExprDGE.Rd
man/doMergeCCA.Rd
man/doMergeSimple.Rd
man/find_peaks.Rd
man/frac_to_numeric.Rd
man/ggUMAP.Rd
man/is.even.Rd
man/is.odd.Rd
man/quickTabulate.Rd
man/range01.Rd
man/range01b.Rd
tests/testdata/10xCounts/CellRanger2/raw_gene_bc_matrices/cellRanger-3204293/barcodes.tsv
tests/testdata/10xCounts/CellRanger2/raw_gene_bc_matrices/cellRanger-3204293/genes.tsv
tests/testdata/10xCounts/CellRanger2/raw_gene_bc_matrices/cellRanger-3204293/matrix.mtx
tests/testdata/10xCounts/CellRanger3/raw_feature_bc_matrix/barcodes.tsv.gz
tests/testdata/10xCounts/CellRanger3/raw_feature_bc_matrix/features.tsv.gz
tests/testdata/10xCounts/CellRanger3/raw_feature_bc_matrix/matrix.mtx.gz
tests/testdata/cellHashing/umi_count/barcodes.tsv.gz
tests/testdata/cellHashing/umi_count/features.tsv.gz
tests/testdata/cellHashing/umi_count/matrix.mtx.gz
tests/testdata/seuratOutput.rds
tests/testthat.R
tests/testthat/test-citeseq.R
tests/testthat/test-classification.R
tests/testthat/test-data.R
tests/testthat/test-genealias.R
tests/testthat/test-genealiasing.R
tests/testthat/test-seurat-merge.R
tests/testthat/test-seurat.R
tests/testthat/test-singleR.R
