API for vertesy/Seurat.utils
Seurat.utils - utility functions for Seurat
| Global functions | |
|---|---|
| .Annotate4Plotly3D | Man page Source code |
| .FindCommandInObject | Man page Source code |
| .adjustLayout | Man page Source code |
| .checkListElements | Man page Source code |
| .check_and_rename | Man page Source code |
| .estMinimumFC | Man page Source code |
| .getNrCores | Man page Source code |
| .getNrPCs | Man page Source code |
| .getNrScaledFeatures | Man page Source code |
| .getRegressionVariablesForScaleData | Man page Source code |
| .metaColnames | Man page Source code |
| .parseBasicObjStats | Man page Source code |
| .parseKeyParams | Man page Source code |
| .parseRegressionVariablesForScaleData | Source code |
| .replace_by_most_frequent_categories | Man page Source code |
| .saveRDS.compress.in.BG | Man page Source code |
| Add.DE.combined.score | Man page Source code |
| AddNewAnnotation | Man page Source code |
| Annotate4Plotly3D | Source code |
| AreTheseCellNamesTheSame | Man page Source code |
| AutoLabel.KnownMarkers | Man page Source code |
| AutoLabelTop.logFC | Man page Source code |
| AutoNumber.by.PrinCurve | Man page Source code |
| AutoNumber.by.UMAP | Man page Source code |
| BackupReduction | Man page Source code |
| Calc.Cor.Seurat | Man page Source code |
| CalculateFractionInTrome | Man page Source code |
| Convert10Xfolders | Man page Source code |
| Convert10Xfolders.old | Man page Source code Source code |
| Convert10Xfolders_v1 | Man page Source code |
| ConvertDropSeqfolders | Man page Source code |
| Create.MiscSlot | Man page Source code |
| DimPlot.ClusterNames | Man page Source code |
| DiscretePaletteSafe | Man page Source code |
| FindCorrelatedGenes | Man page Source code |
| FlipReductionCoordinates | Man page Source code |
| GetClusteringRuns | Man page Source code |
| GetMostVarGenes | Man page Source code |
| GetNamedClusteringRuns | Man page Source code |
| GetNumberOfClusters | Man page Source code |
| GetOrderedClusteringRuns | Man page Source code |
| GetTopMarkers | Man page Source code |
| GetTopMarkersDF | Man page Source code |
| GetUpdateStats | Man page Source code |
| HGNC.EnforceUnique | Man page Source code |
| IntersectGeneLsWithObject | Man page Source code |
| LoadAllSeurats | Man page Source code |
| PctCellsAboveX | Man page Source code |
| PctCellsExpressingGenes | Man page Source code |
| Percent.in.Trome | Source code |
| PercentInTranscriptome | Man page Source code |
| Plot3D.ListOfCategories | Man page Source code |
| Plot3D.ListOfGenes | Man page Source code |
| PlotFilters | Man page Source code |
| PlotTopGenes | Man page Source code |
| PlotTopGenesPerCluster | Man page Source code |
| PlotUpdateStats | Man page Source code |
| PrctCellExpringGene | Man page Source code |
| RecallReduction | Man page Source code |
| RelabelSmallCategories | Man page Source code |
| RemoveGenesSeurat | Man page Source code |
| RenameClustering | Man page Source code |
| RenameGenesSeurat | Man page Source code |
| SavePlotlyAsHtml | Man page Source code |
| SelectHighlyExpressedGenesq99 | Man page Source code |
| SetupReductionsNtoKdimensions | Man page Source code |
| SeuratColorVector | Man page Source code |
| SmallestNonAboveX | Man page Source code |
| StoreAllMarkers | Man page Source code |
| StoreTop25Markers | Man page Source code |
| UpdateGenesSeurat | Man page Source code |
| UpdateSeuratObjectProperly | Man page Source code |
| add.meta.tags | Man page Source code |
| addGeneClassFractions | Man page Source code |
| addMetaDataSafe | Man page Source code |
| addMetaFraction | Man page Source code |
| addToMiscOrToolsSlot | Man page Source code |
| addTranslatedMetadata | Man page Source code |
| calc.cluster.averages | Man page Source code |
| calc.q99.Expression.and.set.all.genes | Man page Source code |
| calculateAverageMetaData | Man page Source code |
| calculatePercentageMatch | Man page Source code |
| cellID_to_cellType | Source code |
| cellID_to_cellType_v1 | Source code |
| check.genes | Man page Source code |
| clUMAP | Man page Source code |
| clip10Xcellname | Man page Source code |
| compareVarFeaturesAndRanks | Man page Source code |
| copyCompleteToolsSlots | Man page Source code |
| copyMiscElements | Man page Source code |
| countEnrichedDepletedGenes | Man page Source code |
| countRelevantEnrichments | Man page Source code |
| create.metadata.vector | Man page Source code |
| create_scCombinedMeta | Man page Source code |
| downsampleListSeuObjsNCells | Man page Source code |
| downsampleListSeuObjsPercent | Man page Source code |
| downsampleSeuObj | Man page Source code |
| downsampleSeuObj.and.Save | Man page Source code |
| downsampleSeuObjByIdentAndMaxcells | Man page Source code |
| dropLevelsSeurat | Man page Source code |
| filterCodingGenes | Man page Source code |
| filterExpressedGenes | Man page Source code |
| filterGoEnrichment | Man page Source code |
| find10XoutputFolders | Man page Source code |
| find_prefix_in_cell_IDs | Man page Source code |
| fix.orig.ident | Man page Source code |
| fixZeroIndexing.seurat | Man page Source code |
| gene.name.check | Man page Source code |
| geneExpressionLevelPlots | Source code |
| get.clustercomposition | Source code |
| getCellIDs.from.meta | Man page Source code |
| getClusterColors | Man page Source code |
| getClusterNames | Man page Source code |
| getDiscretePalette | Man page Source code |
| getDiscretePaletteObj | Man page Source code |
| getMedianMetric.lsObj | Man page Source code |
| getMetaColnames | Man page Source code |
| getMetadataColumn | Man page Source code |
| get_levels_seu | Man page Source code |
| gg_color_hue | Man page Source code |
| heatmap_calc_clust_median | Man page Source code |
| isave.RDS | Man page Source code |
| isave.image | Man page Source code |
| jJaccardIndexBinary | Man page Source code |
| jJaccardIndexVec | Man page Source code |
| jPairwiseJaccardIndex | Man page Source code |
| jPairwiseJaccardIndexList | Man page Source code |
| jPresenceMatrix | Man page Source code |
| load10Xv3 | Man page Source code |
| make10Xcellname | Man page Source code |
| matchBestIdentity | Man page Source code |
| merge_seurat_metadata | Man page Source code |
| metaColnameExists | Man page Source code |
| multiFeatureHeatmap.A4 | Source code |
| multiFeaturePlot.A4 | Man page Source code |
| multiSingleClusterHighlightPlots.A4 | Man page Source code |
| multi_clUMAP.A4 | Man page Source code |
| panelCorPearson | Man page Source code |
| parallel.computing.by.future | Man page Source code |
| plot.Gene.Cor.Heatmap | Man page Source code |
| plot.UMAP.tSNE.sidebyside | Man page Source code |
| plot.expression.rank.q90 | Man page Source code |
| plot3D.umap | Man page Source code |
| plot3D.umap.gene | Man page Source code |
| plotAndSaveHeatmaps | Man page Source code |
| plotClustSizeDistr | Man page Source code |
| plotGeneExpHist | Source code |
| plotGeneExprHistAcrossCells | Man page Source code |
| plotGeneExpressionInBackgroundHist | Man page Source code |
| plotMetadataCategPie | Man page Source code |
| plotMetadataCorHeatmap | Man page Source code |
| plotMetadataMedianFractionBarplot | Man page Source code |
| plotQUMAPsInAFolder | Man page Source code |
| plotTheSoup | Man page Source code |
| prefix_cells_seurat | Man page Source code |
| processSeuratObject | Man page Source code |
| qClusteringUMAPS | Man page Source code |
| qFeatureScatter | Man page Source code |
| qGeneExpressionUMAPS | Man page Source code |
| qMarkerCheck.BrainOrg | Man page Source code |
| qQC.plots.BrainOrg | Man page Source code |
| qSeuViolin | Man page Source code |
| qUMAP | Man page Source code |
| qqSaveGridA4 | Man page Source code |
| qsave.image | Man page Source code |
| read10x | Man page Source code |
| recall.all.genes | Man page Source code |
| recall.genes.ls | Man page Source code |
| recall.meta.tags.n.datasets | Man page Source code |
| recall.parameters | Man page Source code |
| regress_out_and_recalculate_seurat | Man page Source code |
| removeCellsByUmap | Man page Source code |
| removeClustersAndDropLevels | Man page Source code |
| removeLayersByPattern | Man page Source code |
| removeResidualSmallClusters | Man page Source code |
| removeScaleData | Man page Source code |
| renameAzimuthColumns | Man page Source code |
| renameSmallCategories | Man page Source code |
| runDGEA | Man page Source code |
| sampleNpc | Man page Source code |
| save.parameters | Man page Source code |
| save2plots.A4 | Man page Source code |
| save2umaps.A4 | Source code |
| save4plots.A4 | Man page Source code |
| save4umaps.A4 | Source code |
| saveLsSeuratMetadata | Man page Source code |
| scBarplot.CellFractions | Man page Source code |
| scBarplot.CellsPerCluster | Man page Source code |
| scBarplot.CellsPerObject | Man page Source code |
| scBarplot.FractionAboveThr | Man page Source code |
| scBarplot.FractionBelowThr | Man page Source code |
| scBarplotEnrichr | Man page Source code |
| scBarplotStackedMetaCateg_List | Man page Source code |
| scCalcPCAVarExplained | Man page Source code |
| scEnhancedVolcano | Man page Source code |
| scGOEnrichment | Man page Source code |
| scPieClusterDistribution | Man page Source code |
| scPlotPCAvarExplained | Man page Source code |
| set.all.genes | Source code |
| set.mm | Man page Source code |
| seu.Make.Cl.Label.per.cell | Man page Source code |
| seu.RemoveMetadata | Man page Source code |
| seu.add.meta.from.table | Man page Source code |
| seu.add.meta.from.vector | Source code |
| seu.map.and.add.new.ident.to.meta | Man page Source code |
| shorten_clustering_names | Man page Source code |
| showMiscSlots | Man page Source code |
| showToolsSlots | Man page Source code |
| sparse.cor | Man page Source code |
| suPlotVariableFeatures | Man page Source code |
| subsetSeuObjByIdent | Man page Source code |
| transferLabelsSeurat | Man page Source code |
| transferMetadata | Man page Source code |
| umapHiLightSel | Man page Source code |
| umapNamedClusters | Man page Source code |
| whitelist.subset.ls.Seurat | Man page Source code |
| writeCombinedMetadataToTsvFromLsObj | Man page Source code |
| ww.calc_helper | Man page Source code |
| ww.check.quantile.cutoff.and.clip.outliers | Man page Source code |
| ww.get.1st.Seur.element | Man page Source code |
| xread | Man page Source code |
| xsave | Man page Source code |
