Man pages for bimberlabinternal/CellMembrane
A package with high-level wrappers and pipelines for single-cell RNA-seq tools
| AddNewMetaColumn | Add a new Seurat object metadata column based on current... |
| AppendCiteSeq | Read/Append CITE-seq/ADT data to a Seurat Object |
| AppendPerCellSaturation | Append Per Cell Saturation |
| AppendPerCellSaturationInBulk | Append Per Cell Saturation in Bulk |
| AvgExpression | Calculate Avg Expression |
| CalculateClusterEnrichment | CalculateClusterEnrichment |
| CalculatePercentMito | Calculate Mitochrondrial Percentage |
| CalculateTcrDiversity | Calculate TCR diversity |
| CalculateTcrDiversityFromSeurat | Calculate TCR diversity from a seurat object |
| CalculateUcellPerFeature | CalculateUcellPerFeature |
| cdGenes | Table mapping gene symbol to CD gene name |
| CellCycleScoring_UCell | CellCycleScoring_UCell |
| CiteSeqDimRedux.Dist | Perform DimRedux on CiteSeq using euclidean distance |
| CiteSeqDimRedux.PCA | Perform DimRedux on CiteSeq using PCA input |
| ClrNormalizeByGroup | ClrNormalizeByGroup |
| ClusteredDotPlot | ClusteredDotPlot |
| ConstructEnrichmentDataFrameAndDoStatistics | ConstructEnrichmentDataFrameAndDoStatistics |
| CreateSeuratObj | Wrapper around Seurat::CreateSeuratObject |
| DesignModelMatrix | DesignModelMatrix |
| DetectCellStructuresBasedOnCellType | DetectCellStructuresBasedOnCellType |
| DoLdaParameterScan | DoLdaParameterScan |
| dot-addRegulationInformationAndFilterDEGs | .addRegulationInformationAndFilterDEGs |
| dot-GenerateSizeFactor | .GenerateSizeFactor |
| dot-RemoveSpecialCharacters | RemoveSpecialCharacters |
| dot-swapContrast | .swapContrast |
| dot-UpdateGeneModel | Update Gene Model |
| DownsampleSeurat | Downsample Seurat |
| FeaturePlotAcrossReductions | FeaturePlot Across Reductions |
| FilterCloneNames | FilterCloneNames |
| FilterPseudobulkContrasts | FilterPseudobulkContrasts |
| FilterRawCounts | Perform Cell Filtering on the cells of the seurat object |
| FindClustersAndDimRedux | Find Clusters And Perform DimRedux |
| FindDoublets | Find Doublets using scDblFinder |
| Find_Markers | Find_Markers |
| FitRegularizedClassificationGlm | FitRegularizedClassificationGlm |
| GetAssayMetadataSlotName | GetAssayMetadataSlotName |
| GetChiDF | Create a dataframe with chi-squared statistics of clones |
| GetG2MGenes | Get G2M Phase Genes |
| GetGeneIds | Retrieve the gene IDs from a seuratObj created using... |
| GetMsigdbGeneSet | GetMsigdbGeneSet |
| GetSeed | Get random seed |
| GetSPhaseGenes | Get S Phase Genes |
| GetXYDataFromPlot | GetXYDataFromPlot |
| HasSplitLayers | HasSplitLayers |
| HighlightCellsOnSeuratPlot | HighlightCellsOnSeuratPlot |
| InspectSeurat | Inspect Seurat |
| LogNormalizeUsingAlternateAssay | LogNormalizeUsingAlternateAssay |
| MakeEnrichmentDotPlot | MakeEnrichmentDotPlot |
| MergeSeuratObjs | Merge Seurat Objects |
| MergeSplitLayers | MergeSplitLayers |
| NanoString_Housekeeping_Normalization | NanoString_Housekeeping_Normalization |
| NormalizeAndScale | Run the primary seurat processing steps. |
| PerformDifferentialExpression | PerformDifferentialExpression |
| PerformEmptyDropletFiltering | PerformEmptyDropletFiltering |
| PerformGlmFit | PerformGlmFit |
| PerformIntegration | PerformIntegration |
| PlotAverageAdtCounts | Plot Average ADT counts |
| PlotSdaCellScores | Plot SDA Cell Scores |
| Plot_SDAScoresPerFeature | Plot SDA Cell Scores By Feature |
| PlotSeuratVariables | Plot Seurat Variables |
| PredictScTourPseudotime | PredictScTourPseudotime |
| PseudobulkingBarPlot | PseudobulkingBarPlot |
| PseudobulkingDEHeatmap | PseudobulkingDEHeatmap |
| PseudobulkSeurat | Pseudobulk Seurat |
| Q3_Normalization | Q3_Normalization |
| QuantifyTcrClones | Append Clone Properties |
| ReadAndFilter10xData | Read and Filter 10X files. |
| RegressCellCycle | Regress Cell Cycle |
| RenameUsingCD | Rename a vector of genes using CD nomenclature |
| ResolveLocGenes | Resolve NCBI Loc Genes |
| RLE_Plot | RLE_Plot |
| RunCoNGA | Run CoNGA |
| RunCsCore | Run CS-CORE |
| RunEscape | Run escape ssGSEA |
| RunFilteredContrasts | RunFilteredContrasts |
| runLDA | Runs LDA Model |
| RunPcaSteps | Run Seurat PCA |
| RunPHATE | Run PHATE |
| RunSDA | RunSDA |
| RunSeuratWnn | Perform Seurat WNN on CiteSeq |
| RunSingleR | Run SingleR For A Seurat Object |
| RunUmapOnSDA | Run UMAP using SDA results |
| RUVg_Housekeeping_Normalization | RUVg_Housekeeping_Normalization |
| ScaleFeaturesIfNeeded | Scale Features If Needed |
| ScoreCellCycle | Score Cell Cycle |
| SDA_GO_Enrichment | Compute and score GO enrichment for SDA components |
| SDAToSeuratMetadata | SDAToSeuratMetadata |
| SDAToSeuratReduction | SDAToSeuratReduction |
| SetSeed | Set random seed |
| SeuratToCoNGA | SeuratToCoNGA |
| SpatialNormalizeByGroup | SpatialNormalizeByGroup |
| SplitSeurat | Split Seurat |
| SubsetSeurat | Subset Seurat Using String Expressions |
| TrainSctourModel | TrainSctourModel |
| UpdateMacaqueMmul10NcbiGeneSymbols | Update Seurat Object Gene Model From Monkey LOCs to Human... |
| WriteCellBarcodes | Write Cell Barcodes |
| WriteSummaryMetrics | Write Summary Metrics |
