Man pages for vertesy/Seurat.utils
Seurat.utils - utility functions for Seurat
| Add.DE.combined.score | Add.DE.combined.score |
| addGeneClassFractions | Add Meta Data for Gene-Class Fractions |
| addMetaDataSafe | Add Metadata to a Seurat object, safely with Checks |
| addMetaFraction | addMetaFraction |
| add.meta.tags | add.meta.tags |
| AddNewAnnotation | AddNewAnnotation |
| addToMiscOrToolsSlot | Add to Misc or Tools Slot |
| addTranslatedMetadata | Add Translated Metadata to a Seurat Object |
| AreTheseCellNamesTheSame | AreTheseCellNamesTheSame |
| AutoLabel.KnownMarkers | AutoLabel.KnownMarkers |
| AutoLabelTop.logFC | AutoLabelTop.logFC |
| AutoNumber.by.PrinCurve | AutoNumber.by.PrinCurve |
| AutoNumber.by.UMAP | Relabel Cluster Numbers Along a UMAP (or tSNE) Axis |
| BackupReduction | Backup Dimensionality Reduction Data |
| calc.cluster.averages | calc.cluster.averages |
| Calc.Cor.Seurat | Calc.Cor.Seurat |
| calc.q99.Expression.and.set.all.genes | calc.q99.Expression.and.set.all.genes |
| calculateAverageMetaData | Calculate Average Metadata for Seurat Object |
| CalculateFractionInTrome | Calculate Fraction of Genes in Transcriptome |
| calculatePercentageMatch | Calculate the Percentage of Matches per Category |
| check.genes | Check if Gene Names exist in Seurat Object or HGNC Database |
| clip10Xcellname | Clip Suffixes from 10X Cell Names |
| clUMAP | clUMAP - Quick Visualization of Clustering Results with UMAP... |
| compareVarFeaturesAndRanks | Compare variable features and their ranks in two Seurat... |
| Convert10Xfolders | Convert10Xfolders |
| Convert10Xfolders.old | Convert10Xfolders.old |
| Convert10Xfolders_v1 | Convert10Xfolders - legacy version |
| ConvertDropSeqfolders | ConvertDropSeqfolders |
| copyCompleteToolsSlots | Copy Tools Slots from Multiple Seurat Objects |
| copyMiscElements | Copy Specified Elements from One Seurat Object's @misc to... |
| countEnrichedDepletedGenes | Count Enriched and Depleted Genes |
| countRelevantEnrichments | Count Relevant Enrichments |
| create.metadata.vector | Create a Metadata Vector |
| Create.MiscSlot | Create.MiscSlot |
| create_scCombinedMeta | Create Single-Cell Metadata Object for a collection of Seurat... |
| DimPlot.ClusterNames | DimPlot.ClusterNames |
| DiscretePaletteSafe | Safely generate a Discrete color palette. |
| dot-adjustLayout | Adjust Layout Parameters for multi* plotting fucntions |
| dot-Annotate4Plotly3D | .Annotate4Plotly3D |
| dot-check_and_rename | Check and Rename Gene Names in Seurat Assay Object |
| dot-checkListElements | Check List Elements |
| dot-estMinimumFC | Estimate Minimum Log2-Based Fold Change |
| dot-FindCommandInObject | Find Command in Seurat Object by Partial Match |
| dot-getNrCores | Get the number of CPUs to use for CBE processing |
| dot-getNrPCs | Get number of principal components |
| dot-getNrScaledFeatures | Get number of scaled features |
| dot-getRegressionVariablesForScaleData | Parse regression variables for name tagging |
| dot-metaColnames | Extract meta.data Column Names Matching a Pattern |
| dot-parseBasicObjStats | Parse basic obj stats |
| dot-parseKeyParams | Parse key parameters from an object and format as a string |
| dot-replace_by_most_frequent_categories | Find Best Match: Replace Categories by the Most Frequent... |
| dot-saveRDS.compress.in.BG | .saveRDS.compress.in.BG |
| downsampleListSeuObjsNCells | Downsample a List of Seurat Objects to a Specific Number of... |
| downsampleListSeuObjsPercent | Downsample a List of Seurat Objects to a Fraction |
| downsampleSeuObj | downsampleSeuObj |
| downsampleSeuObj.and.Save | downsampleSeuObj.and.Save |
| downsampleSeuObjByIdentAndMaxcells | Sample max number of Cells From each identity in a Seurat... |
| dropLevelsSeurat | dropLevelsSeurat |
| filterCodingGenes | Filter Coding Gene Symbols (or any matching input Patterns) |
| filterExpressedGenes | Filter and Sort Gene Expression List Based on Specified Genes... |
| filterGoEnrichment | Filter GO Enrichment Results |
| find10XoutputFolders | Find 'Outs' Subdirectories in Specified Subdirectories |
| FindCorrelatedGenes | FindCorrelatedGenes |
| find_prefix_in_cell_IDs | Check Prefix in Seurat Object Cell IDs |
| fix.orig.ident | fix.orig.ident |
| fixZeroIndexing.seurat | Fix Zero Indexing in Seurat Clustering |
| FlipReductionCoordinates | Flip Reduction Coordinates |
| gene.name.check | Check Gene Names in Seurat Object |
| getCellIDs.from.meta | getCellIDs.from.meta |
| getClusterColors | Regenerate Cluster Colors from a Seurat Object |
| GetClusteringRuns | GetClusteringRuns |
| getClusterNames | Retrieve Cluster Names |
| getDiscretePalette | Safely generate a discrete color palette (NA). |
| getDiscretePaletteObj | Generate a Discrete Color Palette for Seurat Clusters |
| get_levels_seu | Get Unique Levels of a Seurat Object Ident Slot |
| getMedianMetric.lsObj | getMedianMetric.lsObj |
| getMetaColnames | Get Metadata Column Names Matching Pattern |
| getMetadataColumn | getMetadataColumn |
| GetMostVarGenes | Retrieve the Top Variable Genes from a Seurat Object |
| GetNamedClusteringRuns | GetNamedClusteringRuns |
| GetNumberOfClusters | GetNumberOfClusters |
| GetOrderedClusteringRuns | GetOrderedClusteringRuns |
| GetTopMarkers | Get Top Differential Expression Markers from DGEA Results |
| GetTopMarkersDF | Get Top Differential Expression Genes Data Frame |
| GetUpdateStats | Gene Symbol Update Statistics |
| gg_color_hue | Reproduce the ggplot2 default color palette |
| heatmap_calc_clust_median | Calculate and plot heatmap of cluster medians |
| HGNC.EnforceUnique | Enforce Unique HGNC Gene Symbols |
| IntersectGeneLsWithObject | Intersect Genes with Seurat Object |
| isave.image | isave.image |
| isave.RDS | isave.RDS |
| jJaccardIndexBinary | jJaccardIndexBinary |
| jJaccardIndexVec | jJaccardIndexVec |
| jPairwiseJaccardIndex | jPairwiseJaccardIndex |
| jPairwiseJaccardIndexList | jPairwiseJaccardIndexList |
| jPresenceMatrix | jPresenceMatrix |
| load10Xv3 | Load 10X Genomics Version 3 Data |
| LoadAllSeurats | LoadAllSeurats |
| make10Xcellname | Add Suffix to Cell Names (e.g. lane suffix: _1) |
| matchBestIdentity | Match and Translate Best Identity |
| merge_seurat_metadata | Merge Seurat Metadata |
| metaColnameExists | Check if a Column Exists in the Metadata of an S4 Object |
| multi_clUMAP.A4 | Plot multiple categorical variables in combined UMAPs |
| multiFeaturePlot.A4 | multiFeaturePlot.A4 |
| multiSingleClusterHighlightPlots.A4 | Generate Cluster Highlight UMAPs compiled into A4 pages |
| panelCorPearson | Display Correlation Values in Pairs Plot |
| parallel.computing.by.future | parallel.computing.by.future |
| PctCellsAboveX | Percentage of Cells Above Threshold |
| PctCellsExpressingGenes | PctCellsExpressingGenes |
| PercentInTranscriptome | Gene Expression as Fraction of Total UMI Counts |
| Plot3D.ListOfCategories | Plot3D.ListOfCategories |
| Plot3D.ListOfGenes | Plot3D.ListOfGenes |
| plot3D.umap | plot3D.umap |
| plot3D.umap.gene | plot3D.umap.gene |
| plotAndSaveHeatmaps | Plot and Save Heatmaps from Metadata Calculation Results |
| plotClustSizeDistr | Cluster Size Distribution Plot (Barplot or Histogram) |
| plot.expression.rank.q90 | plot.expression.rank.q90 |
| PlotFilters | Plot filtering thresholds and distributions |
| plot.Gene.Cor.Heatmap | Plot Gene Correlation Heatmap |
| plotGeneExpressionInBackgroundHist | Histogram All Genes' Expression Level and a Highlighted Gene |
| plotGeneExprHistAcrossCells | Histogram of Gene / Geneset Aggregate Expression Across Cells |
| plotMetadataCategPie | Plot Metadata Category Pie Chart |
| plotMetadataCorHeatmap | Plot Metadata Correlation Heatmap |
| plotMetadataMedianFractionBarplot | plotMetadataMedianFractionBarplot |
| plotQUMAPsInAFolder | Plot qUMAPs for Genes in a Folder |
| plotTheSoup | plotTheSoup |
| PlotTopGenes | Plot Top Genes |
| PlotTopGenesPerCluster | Plot Top N Differentially Expressed Genes Per Cluster |
| plot.UMAP.tSNE.sidebyside | plot.UMAP.tSNE.sidebyside |
| PlotUpdateStats | PlotUpdateStats |
| PrctCellExpringGene | Proportion of Cells Expressing Given Genes |
| prefix_cells_seurat | Add Prefixes to Cell Names in Seurat Objects |
| processSeuratObject | Process Seurat Objects in Parallel |
| qClusteringUMAPS | Quick Clustering UMAPs on A4 Page |
| qFeatureScatter | Scatter Plot of Two Features in Seurat Object |
| qGeneExpressionUMAPS | Quickly Draw 4 Gene Expression UMAPs on an A4 Page |
| qMarkerCheck.BrainOrg | Quickly Plot Key Markers in Brain Organoids |
| qQC.plots.BrainOrg | Quickly Plot Key QC Markers in Brain Organoids |
| qqSaveGridA4 | qqSaveGridA4 |
| qsave.image | Save workspace - qsave.image |
| qSeuViolin | Create a Violin Plot for a Seurat Object Feature and save the... |
| qUMAP | Quick UMAP Visualization of Gene Expression and automatically... |
| read10x | Load 10X Genomics Data as Seurat Object |
| recall.all.genes | Recall all.genes global variable from a Seurat object |
| recall.genes.ls | recall.genes.ls |
| recall.meta.tags.n.datasets | recall.meta.tags.n.datasets |
| recall.parameters | recall.parameters |
| RecallReduction | Recall Dimensionality Reduction from backup slot |
| regress_out_and_recalculate_seurat | Regress Out and Recalculate Seurat |
| RelabelSmallCategories | Relabel Small Categories / Clusters |
| removeCellsByUmap | Remove Cells by Dimension Reduction |
| removeClustersAndDropLevels | Remove Clusters and Drop Levels from a List of Seurat Objects |
| RemoveGenesSeurat | Remove Specific Genes from a Seurat Object |
| removeLayersByPattern | Remove Layers from Seurat Object by Pattern |
| removeResidualSmallClusters | Remove Residual Small Clusters from a Seurat Object |
| removeScaleData | Remove Scale Data from Seurat Objects |
| renameAzimuthColumns | Rename Azimuth Columns in Seurat Object |
| RenameClustering | RenameClustering |
| RenameGenesSeurat | Rename Gene Symbols in a Seurat Object |
| renameSmallCategories | Rename Small Categories in Seurat Object Metadata |
| runDGEA | Run Differential Gene Expression Analysis (DGEA) |
| sampleNpc | Sample N % of a dataframe (obj@metadata), and return rownames... |
| save2plots.A4 | Save Two Plots on One A4 Page |
| save4plots.A4 | Save Four Plots on One A4 Page |
| saveLsSeuratMetadata | Save Metadata from a List of Seurat Objects |
| save.parameters | Save Parameters to Seurat Object |
| SavePlotlyAsHtml | SavePlotlyAsHtml |
| scBarplot.CellFractions | Generate Barplot of Cell Fractions |
| scBarplot.CellsPerCluster | Barplot of Fraction of Cells per Cluster |
| scBarplot.CellsPerObject | Barplot of Cells Per Seurat Object |
| scBarplotEnrichr | Barplot GO Enrichment Results by enrichplot |
| scBarplot.FractionAboveThr | Barplot the Fraction of Cells Above Threshold per Cluster |
| scBarplot.FractionBelowThr | Fraction of Cells Below Threshold per Cluster |
| scBarplotStackedMetaCateg_List | Stacked Barplot of Metadata Categories for List of Seurat... |
| scCalcPCAVarExplained | Calculate the percent of variation explained by individual... |
| scEnhancedVolcano | scEnhancedVolcano |
| scGOEnrichment | Perform GO Enrichment Analysis |
| scPieClusterDistribution | scPieClusterDistribution |
| scPlotPCAvarExplained | Plot the percent of variation explained by individual PC's |
| SelectHighlyExpressedGenesq99 | Intersect Genes with the List of Noticeably Expressed Genes |
| set.mm | set.mm |
| SetupReductionsNtoKdimensions | SetupReductionsNtoKdimensions |
| seu.add.meta.from.table | seu.add.meta.from.table |
| seu.Make.Cl.Label.per.cell | Create Cluster Labels for Each Cell |
| seu.map.and.add.new.ident.to.meta | seu.map.and.add.new.ident.to.meta |
| SeuratColorVector | Regenerate Color Scheme for Clusters in Seurat Object as a... |
| seu.RemoveMetadata | seu.RemoveMetadata |
| shorten_clustering_names | Shorten Clustering Names |
| showMiscSlots | Display Slots in the @misc of an Seurat Object |
| showToolsSlots | Display Slots in the @tools of an Seurat Object |
| SmallestNonAboveX | SmallestNonAboveX |
| sparse.cor | Calculate Sparse Correlation Matrix |
| StoreAllMarkers | Store All Differential Expression Markers |
| StoreTop25Markers | Save Top 25 Markers per Cluster |
| subsetSeuObjByIdent | Subset a Seurat Object by Identity |
| suPlotVariableFeatures | suPlotVariableFeatures for Single Seurat Object |
| transferLabelsSeurat | Transfer labels from a reference Seurat object to a query... |
| transferMetadata | Transfer Multiple Metadata Columns Between Two Seurat Objects |
| umapHiLightSel | Highlight Selected Clusters on UMAP |
| umapNamedClusters | Plot and Save UMAP without legend |
| UpdateGenesSeurat | Update Gene Symbols in a Seurat Object |
| UpdateSeuratObjectProperly | Update Seurat Object Properly, including Assays and DimReducs |
| whitelist.subset.ls.Seurat | whitelist.subset.ls.Seurat |
| writeCombinedMetadataToTsvFromLsObj | Combine Metadata from a list of Seurat objects and Write to... |
| ww.calc_helper | Helper to calculate Cell Expression Proportion for Gene |
| ww.check.quantile.cutoff.and.clip.outliers | Check Quantile Cutoff and Clip Outliers |
| ww.get.1st.Seur.element | Get the First Seurat Object from a List of Seurat Objects |
| xread | Read an R Object Using 'qs' Package for Fast Decompression |
| xsave | Save an R Object Using 'qs' Package for Fast Compressed... |
