API for bimberlabinternal/CellMembrane
A package with high-level wrappers and pipelines for single-cell RNA-seq tools
| Global functions | |
|---|---|
| .AddCompStats | Source code |
| .AddFeatureMetadata | Source code |
| .AppendSaturation | Source code |
| .AppendScTourAsReduction | Source code |
| .CalcPerCellSaturation | Source code |
| .CheckColnamesAreNumeric | Source code |
| .CheckDuplicatedCellNames | Source code |
| .ClearSeuratCommands | Source code |
| .DoMergeSimple | Source code |
| .DoNormalizationLda | Source code |
| .EnsureCellsPresentInOrder | Source code |
| .EnsureFeaturesInSdaResults | Source code |
| .EnsureFeaturesPresentInOrder | Source code |
| .FilterLowCalls | Source code |
| .FindElbow | Source code |
| .FindLayersToJoin | Source code |
| .FindSeuratElbow | Source code |
| .GenerateSizeFactor | Man page Source code |
| .GetCCGenes | Source code |
| .GetDimsToUse | Source code |
| .GetNonZeroFeatures | Source code |
| .InferBpParam | Source code |
| .InferMatrixDir | Source code |
| .InferPerplexity | Source code |
| .InferPerplexityFromSeuratObj | Source code |
| .LoadCiteSeqData | Source code |
| .MergeAdtWithExisting | Source code |
| .MergeSplitLayersIfNeeded | Source code |
| .NormalizeAndScaleDefault | Source code |
| .NormalizeAndScaleSCTransform | Source code |
| .NormalizeDsbWithEmptyDrops | Source code |
| .NormalizeEscape | Source code |
| .PlotCiteSeqCountData | Source code |
| .PlotVariableFeatures | Source code |
| .PossiblyAddBarcodePrefix | Source code |
| .PossiblyExpandAssay | Source code |
| .PrintQcPlots | Source code |
| .PrintSeuratPlots | Source code |
| .RemoveSpecialCharacters | Man page Source code |
| .RenameAssayFeatures | Source code |
| .ReorderAssayCells | Source code |
| .ReorderAssayFeatures | Source code |
| .RunEscapePca | Source code |
| .RunPHATE | Source code |
| .RunSoupX | Source code |
| .RunUMAP | Source code |
| .SplitIntoBatches | Source code |
| .UpdateGeneModel | Man page Source code |
| .WriteLogMsg | Source code |
| .addRegulationInformationAndFilterDEGs | Man page |
| .normalize | Source code |
| .swapContrast | Man page |
| .threshold | Source code |
| AddNewMetaColumn | Man page Source code |
| AppendCiteSeq | Man page Source code |
| AppendPerCellSaturation | Man page Source code |
| AppendPerCellSaturationInBulk | Man page Source code |
| AvgExpression | Man page Source code |
| CalculateClusterEnrichment | Man page Source code |
| CalculatePercentMito | Man page Source code |
| CalculateTcrDiversity | Man page Source code |
| CalculateTcrDiversityFromSeurat | Man page Source code |
| CalculateUcellPerFeature | Man page |
| CellCycleScoring_UCell | Man page Source code |
| CiteSeqDimRedux.Dist | Man page |
| CiteSeqDimRedux.PCA | Man page |
| ClrNormalizeByGroup | Man page Source code |
| ClusteredDotPlot | Man page Source code |
| ConstructEnrichmentDataFrameAndDoStatistics | Man page Source code |
| CreateSeuratObj | Man page Source code |
| DesignModelMatrix | Man page Source code |
| DetectCellStructuresBasedOnCellType | Man page Source code |
| DimPlot_SingleR | Source code |
| DoLdaParameterScan | Man page Source code |
| DownsampleSeurat | Man page Source code |
| FeaturePlotAcrossReductions | Man page Source code |
| FilterCloneNames | Man page Source code |
| FilterPseudobulkContrasts | Man page Source code |
| FilterRawCounts | Man page Source code |
| FindClustersAndDimRedux | Man page Source code |
| FindDoublets | Man page Source code |
| Find_Markers | Man page Source code |
| FitRegularizedClassificationGlm | Man page |
| GetAssayMetadataSlotName | Man page Source code |
| GetChiDF | Man page Source code |
| GetG2MGenes | Man page Source code |
| GetGeneIds | Man page Source code |
| GetMsigdbGeneSet | Man page Source code |
| GetSPhaseGenes | Man page Source code |
| GetSeed | Man page Source code |
| GetXYAesthetics | Source code |
| GetXYDataFromPlot | Man page Source code |
| HasSplitLayers | Man page Source code |
| HighlightCellsOnSeuratPlot | Man page Source code |
| InspectSeurat | Man page Source code |
| LDAelbowPlot | Source code |
| LogNormalizeUsingAlternateAssay | Man page Source code |
| MakeEnrichmentDotPlot | Man page Source code |
| MergeSeuratObjs | Man page Source code |
| MergeSplitLayers | Man page Source code |
| NanoString_Housekeeping_Normalization | Man page Source code |
| NormalizeAndScale | Man page Source code |
| PerformDifferentialExpression | Man page Source code |
| PerformEmptyDropletFiltering | Man page Source code |
| PerformEmptyDrops | Source code |
| PerformGlmFit | Man page Source code |
| PerformIntegration | Man page Source code |
| PlotAverageAdtCounts | Man page |
| PlotSdaCellScores | Man page Source code |
| PlotSeuratVariables | Man page Source code |
| Plot_CorSDA_Loadings | Source code |
| Plot_SDAScoresPerFeature | Man page Source code |
| PredictScTourPseudotime | Man page Source code |
| PseudobulkSeurat | Man page Source code |
| PseudobulkingBarPlot | Man page |
| PseudobulkingDEHeatmap | Man page |
| Q3_Normalization | Man page Source code |
| QuantifyTcrClones | Man page Source code |
| RLE_Plot | Man page Source code |
| RUVg_Housekeeping_Normalization | Man page Source code |
| ReadAndFilter10xData | Man page Source code |
| RegressCellCycle | Man page Source code |
| RenameUsingCD | Man page Source code |
| ResolveLocGenes | Man page Source code |
| RunCoNGA | Man page Source code |
| RunCsCore | Man page Source code |
| RunEscape | Man page Source code |
| RunFilteredContrasts | Man page Source code |
| RunPHATE | Man page Source code |
| RunPcaSteps | Man page Source code |
| RunSDA | Man page Source code |
| RunSeuratWnn | Man page |
| RunSingleR | Man page Source code |
| RunUmapOnSDA | Man page Source code |
| SDAToSeuratMetadata | Man page Source code |
| SDAToSeuratReduction | Man page Source code |
| SDA_GO_Enrichment | Man page Source code |
| SDA_GO_VolcanoPlot | Source code |
| ScaleFeaturesIfNeeded | Man page Source code |
| ScoreCellCycle | Man page Source code |
| SetSeed | Man page Source code |
| SeuratToCoNGA | Man page Source code |
| SpatialNormalizeByGroup | Man page Source code |
| SplitSeurat | Man page Source code |
| SubsetSeurat | Man page Source code |
| Tabulate_SingleR | Source code |
| TrainSctourModel | Man page Source code |
| UpdateMacaqueMmul10NcbiGeneSymbols | Man page Source code |
| WriteCellBarcodes | Man page Source code |
| WriteSummaryMetrics | Man page Source code |
| `%||%` | Source code |
| cdGenes | Man page |
| nand | Source code |
| nor | Source code |
| runLDA | Man page Source code |
| scale_mat | Source code |
| scale_rows | Source code |
| xnor | Source code |
