Files in bimberlabinternal/CellMembrane
A package with high-level wrappers and pipelines for single-cell RNA-seq tools
.Rbuildignore
.dockerignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yml
.gitignore
CellMembrane.iml
DESCRIPTION
Dockerfile
NAMESPACE
R/Analysis.R
R/CSCore.R
R/CiteSeq.R
R/CoNGA.R
R/Doublets.R
R/LDA.R
R/Phate.R
R/Preprocessing.R
R/PseudoBulk.R
R/SDA.R
R/SeuratUtils.R
R/Seurat_III.R
R/SingleR_Seurat.R
R/Spatial.R
R/Utils.R
R/data.R
R/escape.R
R/sctour.R
R/sysdata.rda
README.md
_pkgdown.yml
data/cdGenes.rda
inst/scripts/PredictScTourPseudotime.py
inst/scripts/TrainScTourModel.py
inst/scripts/calculate_Diversity.py
inst/scripts/run_CoNGA.py
inst/scripts/run_sctour.py
man/AddNewMetaColumn.Rd
man/AppendCiteSeq.Rd
man/AppendPerCellSaturation.Rd
man/AppendPerCellSaturationInBulk.Rd
man/AvgExpression.Rd
man/CalculateClusterEnrichment.Rd
man/CalculatePercentMito.Rd
man/CalculateTcrDiversity.Rd
man/CalculateTcrDiversityFromSeurat.Rd
man/CalculateUcellPerFeature.Rd
man/CellCycleScoring_UCell.Rd
man/CiteSeqDimRedux.Dist.Rd
man/CiteSeqDimRedux.PCA.Rd
man/ClrNormalizeByGroup.Rd
man/ClusteredDotPlot.Rd
man/ConstructEnrichmentDataFrameAndDoStatistics.Rd
man/CreateSeuratObj.Rd
man/DesignModelMatrix.Rd
man/DetectCellStructuresBasedOnCellType.Rd
man/DoLdaParameterScan.Rd
man/DownsampleSeurat.Rd
man/FeaturePlotAcrossReductions.Rd
man/FilterCloneNames.Rd
man/FilterPseudobulkContrasts.Rd
man/FilterRawCounts.Rd
man/FindClustersAndDimRedux.Rd
man/FindDoublets.Rd
man/Find_Markers.Rd
man/FitRegularizedClassificationGlm.Rd
man/GetAssayMetadataSlotName.Rd
man/GetChiDF.Rd
man/GetG2MGenes.Rd
man/GetGeneIds.Rd
man/GetMsigdbGeneSet.Rd
man/GetSPhaseGenes.Rd
man/GetSeed.Rd
man/GetXYDataFromPlot.Rd
man/HasSplitLayers.Rd
man/HighlightCellsOnSeuratPlot.Rd
man/InspectSeurat.Rd
man/LogNormalizeUsingAlternateAssay.Rd
man/MakeEnrichmentDotPlot.Rd
man/MergeSeuratObjs.Rd
man/MergeSplitLayers.Rd
man/NanoString_Housekeeping_Normalization.Rd
man/NormalizeAndScale.Rd
man/PerformDifferentialExpression.Rd
man/PerformEmptyDropletFiltering.Rd
man/PerformGlmFit.Rd
man/PerformIntegration.Rd
man/PlotAverageAdtCounts.Rd
man/PlotSdaCellScores.Rd
man/PlotSeuratVariables.Rd
man/Plot_SDAScoresPerFeature.Rd
man/PredictScTourPseudotime.Rd
man/PseudobulkSeurat.Rd
man/PseudobulkingBarPlot.Rd
man/PseudobulkingDEHeatmap.Rd
man/Q3_Normalization.Rd
man/QuantifyTcrClones.Rd
man/RLE_Plot.Rd
man/RUVg_Housekeeping_Normalization.Rd
man/ReadAndFilter10xData.Rd
man/RegressCellCycle.Rd
man/RenameUsingCD.Rd
man/ResolveLocGenes.Rd
man/RunCoNGA.Rd
man/RunCsCore.Rd
man/RunEscape.Rd
man/RunFilteredContrasts.Rd
man/RunPHATE.Rd
man/RunPcaSteps.Rd
man/RunSDA.Rd
man/RunSeuratWnn.Rd
man/RunSingleR.Rd
man/RunUmapOnSDA.Rd
man/SDAToSeuratMetadata.Rd
man/SDAToSeuratReduction.Rd
man/SDA_GO_Enrichment.Rd
man/ScaleFeaturesIfNeeded.Rd
man/ScoreCellCycle.Rd
man/SetSeed.Rd
man/SeuratToCoNGA.Rd
man/SpatialNormalizeByGroup.Rd
man/SplitSeurat.Rd
man/SubsetSeurat.Rd
man/TrainSctourModel.Rd
man/UpdateMacaqueMmul10NcbiGeneSymbols.Rd
man/WriteCellBarcodes.Rd
man/WriteSummaryMetrics.Rd
man/cdGenes.Rd
man/dot-GenerateSizeFactor.Rd
man/dot-RemoveSpecialCharacters.Rd
man/dot-UpdateGeneModel.Rd
man/dot-addRegulationInformationAndFilterDEGs.Rd
man/dot-swapContrast.Rd
man/runLDA.Rd
tests/testdata/438-21-GEX.rawCounts.2.citeseq/run_report.yaml
tests/testdata/438-21-GEX.rawCounts.2.citeseq/umi_count/barcodes.tsv.gz
tests/testdata/438-21-GEX.rawCounts.2.citeseq/umi_count/features.tsv.gz
tests/testdata/438-21-GEX.rawCounts.2.citeseq/umi_count/matrix.mtx.gz
tests/testdata/512-5-molecule_info.h5
tests/testdata/CellRanger2/raw_gene_bc_matrices/cellRanger-3204293/barcodes.tsv
tests/testdata/CellRanger2/raw_gene_bc_matrices/cellRanger-3204293/genes.tsv
tests/testdata/CellRanger2/raw_gene_bc_matrices/cellRanger-3204293/matrix.mtx
tests/testdata/CellRanger3/raw_feature_bc_matrix/barcodes.tsv.gz
tests/testdata/CellRanger3/raw_feature_bc_matrix/features.tsv.gz
tests/testdata/CellRanger3/raw_feature_bc_matrix/matrix.mtx.gz
tests/testdata/clones_file.txt
tests/testdata/raw_feature_bc_matrix/barcodes.tsv.gz
tests/testdata/raw_feature_bc_matrix/features.tsv.gz
tests/testdata/raw_feature_bc_matrix/matrix.mtx.gz
tests/testdata/raw_feature_bc_matrix/validADTS.32851.metadata.txt
tests/testdata/seuratOutput.rds
tests/testdata/seuratOutputWithTCR.rds
tests/testdata/tcr_df.csv
tests/testthat.R
tests/testthat/test-analysis.R
tests/testthat/test-citeseq.R
tests/testthat/test-conga.R
tests/testthat/test-cscore.R
tests/testthat/test-data.R
tests/testthat/test-doublets.R
tests/testthat/test-escape.R
tests/testthat/test-lda.R
tests/testthat/test-phate.R
tests/testthat/test-pseudobulk.R
tests/testthat/test-sctour.R
tests/testthat/test-sda.R
tests/testthat/test-seurat-manipulation.R
tests/testthat/test-seurat-merge.R
tests/testthat/test-seurat.R
tests/testthat/test-singleR.R
tests/testthat/test-spatial.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/CellMembrane-Tutorial.Rmd
vignettes/Pseudobulking-and-Filtered-Contrasts.Rmd
