Files in vertesy/Seurat.utils

Seurat.utils - utility functions for Seurat

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md CODE_OF_CONDUCT.md CONTRIBUTING.md Deprecated/MULTI-seq.Utils.R Deprecated/Monocle.Utils.R Development/Create_the_Seurat.utils_Package.OLD.R Development/Create_the_Seurat.utils_Package.R Development/Dependencies.R Development/Functions/Cluster.Auto-naming.DE.R Development/Functions/Custom.Functions.for.Slingshot.R Development/Functions/Jaccard.toolkit.R Development/Functions/MULTI-seq.functions.R Development/Functions/Metadata.manipulation.R Development/Functions/Monocle.Utils.R Development/Functions/Plotting.dim.reduction.2D.R Development/Functions/Plotting.dim.reduction.3D.R Development/Functions/Plotting.filtering.R Development/Functions/Plotting.statistics.and.QC.R Development/Functions/Read.Write.Save.Load.functions.R Development/Functions/Seurat.object.manipulations.etc.R Development/Functions/Seurat.update.gene.symbols.HGNC.R Development/Functions/Soup.Analysis.of.ambient.RNA.R Development/Functions/deprecated/Cell.Fractions.Old.R Development/Functions/deprecated/plotting.filtering.old.R Development/Functions/deprecated/tmp.R Development/Seurat.Utils.orig.R Development/config.R Development/old/00.Load.Seurat.Utils.LOCAL.R Development/old/00.Load.Seurat.Utils.WEB.R Example.usage/Visualize.Gene.expression.v2.R Example.usage/deprecated/SoupX.Marker.Analysis.R Example.usage/deprecated/SoupX.decontamination.R Function.Dependencies.md R/Seurat.Utils.Metadata.R R/Seurat.Utils.R R/Seurat.Utils.Visualization.R R/Seurat.utils.less.used.R README.md Vignettes/Auto.Generated.No.Plots/Vignette.Seurat.Utils.Metadata.Rmd Vignettes/Auto.Generated.No.Plots/Vignette.Seurat.Utils.Rmd Vignettes/Auto.Generated.No.Plots/Vignette.Seurat.Utils.Visualization.Rmd Vignettes/scRNAseq_Vignette.2024.10.25.AV.md man/Add.DE.combined.score.Rd man/AddNewAnnotation.Rd man/AreTheseCellNamesTheSame.Rd man/AutoLabel.KnownMarkers.Rd man/AutoLabelTop.logFC.Rd man/AutoNumber.by.PrinCurve.Rd man/AutoNumber.by.UMAP.Rd man/BackupReduction.Rd man/Calc.Cor.Seurat.Rd man/CalculateFractionInTrome.Rd man/Convert10Xfolders.Rd man/Convert10Xfolders.old.Rd man/Convert10Xfolders_v1.Rd man/ConvertDropSeqfolders.Rd man/Create.MiscSlot.Rd man/DimPlot.ClusterNames.Rd man/DiscretePaletteSafe.Rd man/FindCorrelatedGenes.Rd man/FlipReductionCoordinates.Rd man/GetClusteringRuns.Rd man/GetMostVarGenes.Rd man/GetNamedClusteringRuns.Rd man/GetNumberOfClusters.Rd man/GetOrderedClusteringRuns.Rd man/GetTopMarkers.Rd man/GetTopMarkersDF.Rd man/GetUpdateStats.Rd man/HGNC.EnforceUnique.Rd man/IntersectGeneLsWithObject.Rd man/LoadAllSeurats.Rd man/PctCellsAboveX.Rd man/PctCellsExpressingGenes.Rd man/PercentInTranscriptome.Rd man/Plot3D.ListOfCategories.Rd man/Plot3D.ListOfGenes.Rd man/PlotFilters.Rd man/PlotTopGenes.Rd man/PlotTopGenesPerCluster.Rd man/PlotUpdateStats.Rd man/PrctCellExpringGene.Rd man/RecallReduction.Rd man/RelabelSmallCategories.Rd man/RemoveGenesSeurat.Rd man/RenameClustering.Rd man/RenameGenesSeurat.Rd man/SavePlotlyAsHtml.Rd man/SelectHighlyExpressedGenesq99.Rd man/SetupReductionsNtoKdimensions.Rd man/SeuratColorVector.Rd man/SmallestNonAboveX.Rd man/StoreAllMarkers.Rd man/StoreTop25Markers.Rd man/UpdateGenesSeurat.Rd man/UpdateSeuratObjectProperly.Rd man/add.meta.tags.Rd man/addGeneClassFractions.Rd man/addMetaDataSafe.Rd man/addMetaFraction.Rd man/addToMiscOrToolsSlot.Rd man/addTranslatedMetadata.Rd man/calc.cluster.averages.Rd man/calc.q99.Expression.and.set.all.genes.Rd man/calculateAverageMetaData.Rd man/calculatePercentageMatch.Rd man/check.genes.Rd man/clUMAP.Rd man/clip10Xcellname.Rd man/compareVarFeaturesAndRanks.Rd man/copyCompleteToolsSlots.Rd man/copyMiscElements.Rd man/countEnrichedDepletedGenes.Rd man/countRelevantEnrichments.Rd man/create.metadata.vector.Rd man/create_scCombinedMeta.Rd man/dot-Annotate4Plotly3D.Rd man/dot-FindCommandInObject.Rd man/dot-adjustLayout.Rd man/dot-checkListElements.Rd man/dot-check_and_rename.Rd man/dot-estMinimumFC.Rd man/dot-getNrCores.Rd man/dot-getNrPCs.Rd man/dot-getNrScaledFeatures.Rd man/dot-getRegressionVariablesForScaleData.Rd man/dot-metaColnames.Rd man/dot-parseBasicObjStats.Rd man/dot-parseKeyParams.Rd man/dot-replace_by_most_frequent_categories.Rd man/dot-saveRDS.compress.in.BG.Rd man/downsampleListSeuObjsNCells.Rd man/downsampleListSeuObjsPercent.Rd man/downsampleSeuObj.Rd man/downsampleSeuObj.and.Save.Rd man/downsampleSeuObjByIdentAndMaxcells.Rd man/dropLevelsSeurat.Rd man/filterCodingGenes.Rd man/filterExpressedGenes.Rd man/filterGoEnrichment.Rd man/find10XoutputFolders.Rd man/find_prefix_in_cell_IDs.Rd man/fix.orig.ident.Rd man/fixZeroIndexing.seurat.Rd man/gene.name.check.Rd man/getCellIDs.from.meta.Rd man/getClusterColors.Rd man/getClusterNames.Rd man/getDiscretePalette.Rd man/getDiscretePaletteObj.Rd man/getMedianMetric.lsObj.Rd man/getMetaColnames.Rd man/getMetadataColumn.Rd man/get_levels_seu.Rd man/gg_color_hue.Rd man/heatmap_calc_clust_median.Rd man/isave.RDS.Rd man/isave.image.Rd man/jJaccardIndexBinary.Rd man/jJaccardIndexVec.Rd man/jPairwiseJaccardIndex.Rd man/jPairwiseJaccardIndexList.Rd man/jPresenceMatrix.Rd man/load10Xv3.Rd man/make10Xcellname.Rd man/matchBestIdentity.Rd man/merge_seurat_metadata.Rd man/metaColnameExists.Rd man/multiFeaturePlot.A4.Rd man/multiSingleClusterHighlightPlots.A4.Rd man/multi_clUMAP.A4.Rd man/panelCorPearson.Rd man/parallel.computing.by.future.Rd man/plot.Gene.Cor.Heatmap.Rd man/plot.UMAP.tSNE.sidebyside.Rd man/plot.expression.rank.q90.Rd man/plot3D.umap.Rd man/plot3D.umap.gene.Rd man/plotAndSaveHeatmaps.Rd man/plotClustSizeDistr.Rd man/plotGeneExprHistAcrossCells.Rd man/plotGeneExpressionInBackgroundHist.Rd man/plotMetadataCategPie.Rd man/plotMetadataCorHeatmap.Rd man/plotMetadataMedianFractionBarplot.Rd man/plotQUMAPsInAFolder.Rd man/plotTheSoup.Rd man/prefix_cells_seurat.Rd man/processSeuratObject.Rd man/qClusteringUMAPS.Rd man/qFeatureScatter.Rd man/qGeneExpressionUMAPS.Rd man/qMarkerCheck.BrainOrg.Rd man/qQC.plots.BrainOrg.Rd man/qSeuViolin.Rd man/qUMAP.Rd man/qqSaveGridA4.Rd man/qsave.image.Rd man/read10x.Rd man/recall.all.genes.Rd man/recall.genes.ls.Rd man/recall.meta.tags.n.datasets.Rd man/recall.parameters.Rd man/regress_out_and_recalculate_seurat.Rd man/removeCellsByUmap.Rd man/removeClustersAndDropLevels.Rd man/removeLayersByPattern.Rd man/removeResidualSmallClusters.Rd man/removeScaleData.Rd man/renameAzimuthColumns.Rd man/renameSmallCategories.Rd man/runDGEA.Rd man/sampleNpc.Rd man/save.parameters.Rd man/save2plots.A4.Rd man/save4plots.A4.Rd man/saveLsSeuratMetadata.Rd man/scBarplot.CellFractions.Rd man/scBarplot.CellsPerCluster.Rd man/scBarplot.CellsPerObject.Rd man/scBarplot.FractionAboveThr.Rd man/scBarplot.FractionBelowThr.Rd man/scBarplotEnrichr.Rd man/scBarplotStackedMetaCateg_List.Rd man/scCalcPCAVarExplained.Rd man/scEnhancedVolcano.Rd man/scGOEnrichment.Rd man/scPieClusterDistribution.Rd man/scPlotPCAvarExplained.Rd man/set.mm.Rd man/seu.Make.Cl.Label.per.cell.Rd man/seu.RemoveMetadata.Rd man/seu.add.meta.from.table.Rd man/seu.map.and.add.new.ident.to.meta.Rd man/shorten_clustering_names.Rd man/showMiscSlots.Rd man/showToolsSlots.Rd man/sparse.cor.Rd man/suPlotVariableFeatures.Rd man/subsetSeuObjByIdent.Rd man/transferLabelsSeurat.Rd man/transferMetadata.Rd man/umapHiLightSel.Rd man/umapNamedClusters.Rd man/whitelist.subset.ls.Seurat.Rd man/writeCombinedMetadataToTsvFromLsObj.Rd man/ww.calc_helper.Rd man/ww.check.quantile.cutoff.and.clip.outliers.Rd man/ww.get.1st.Seur.element.Rd man/xread.Rd man/xsave.Rd