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A B C D E F G H I K L M P R S T U Z
| aggregateCellsToSamples | Aggregate cells to samples |
| aggregateCols | Aggregate columns |
| aggregateReplicates | Aggregate technical replicates |
| aggregateRows | Aggregate rows |
| alphaSummary | Alpha level cutoff summary statistics |
| alphaThreshold | Alpha threshold |
| alphaThreshold<- | Alpha threshold |
| atomize | Atomize |
| autopadZeros | Autopad zeros |
| barcodeRanksPerSample | Barcode ranks per sample |
| camel | Camel case |
| capitalize | Capitalize |
| cell2sample | Cell-to-sample mappings |
| cellCountsPerCluster | Cell counts per cluster |
| cellTypesPerCluster | Cell types per cluster |
| clusterCellCountsPerSample | Cluster cell counts per sample |
| clusterID | Cluster identifier |
| collapseToString | Collapse to string |
| collectionNames | Gene set collection names |
| collectionNames<- | Gene set collection names |
| contrastName | Contrast name |
| contrastNames | Contrast names |
| contrastNames<- | Contrast names |
| contrastSamples | Samples corresponding to a differential expression contrast |
| convertGenesToSymbols | Convert genes to symbols |
| convertSampleIDsToNames | Convert sample identifiers to names |
| convertSymbolsToGenes | Convert symbols to genes |
| convertTranscriptsToGenes | Convert transcripts to genes |
| deg | Differentially expressed genes |
| diffExp | Differential expression |
| diffExpPerCluster | Differential expression per cluster |
| dotted | Dotted case |
| encode | Encode using run-length encoding |
| enrichedGeneSets | Enriched gene sets |
| export | Export |
| factorize | Factorize |
| filterCells | Filter cells |
| findMarkers | Find cluster-specific marker genes |
| flatFiles | Coerce any S4 object to a list |
| foldChangeToLogRatio | Fold change to log ratio |
| fpkm | Fragments per kilobase per million mapped fragments |
| geneNames | Gene names |
| geometricMean | Geometric mean |
| headtail | Return the first and last parts of an object |
| humanize | Humanize an R object |
| interestingGroups | Interesting groups |
| interestingGroups<- | Interesting groups |
| kebab | Kebab case |
| lfcThreshold | Log2 fold change threshold |
| lfcThreshold<- | Log2 fold change threshold |
| logRatioToFoldChange | Log ratio to fold change |
| mapGenesToIDs | Map genes (gene names) to gene identifiers |
| mapGenesToRownames | Map genes to row names |
| mapGenesToSymbols | Map genes (gene identifiers) to gene names (symbols) |
| markdown | Markdown |
| mcolnames | Metadata column names |
| mcolnames<- | Metadata column names |
| meltCounts | Melt count matrix into long format |
| metrics | Quality control metrics |
| metricsPerSample | Quality control metrics per sample |
| plot5Prime3PrimeBias | Plot 5' to 3' bias |
| plotBarcodeRanks | Plot barcode ranks |
| plotCellCounts | Plot cell counts |
| plotCellCountsPerCluster | Plot cell counts per cluster |
| plotCellTypesPerCluster | Plot cell types per cluster |
| plotCorrelationHeatmap | Correlation heatmap |
| plotCountDensity | Plot count density |
| plotCounts | Plot counts |
| plotCountsPerBiotype | Plot counts per biotype |
| plotCountsPerBroadClass | Plot counts per broad class definition |
| plotCountsPerFeature | Plot counts per feature |
| plotCountsPerGene | Plot counts per gene |
| plotDEGHeatmap | Differentially expressed gene heatmap |
| plotDEGPCA | Plot differentially expressed gene principal component analysis |
| plotDEGUpset | UpSet plot of directional DEG intersections across contrasts |
| plotDot | Dot plot |
| plotEnrichedGeneSets | Plot enriched gene sets |
| plotEnrichedUpset | UpSet plot of directional enriched pathway intersections across contrasts |
| plotExonicMappingRate | Plot exonic mapping rate |
| plotFeature | Plot feature |
| plotFeaturesDetected | Plot features detected |
| plotGenderMarkers | Plot sexually dimorphic gender marker genes |
| plotGeneSaturation | Plot gene detection saturation |
| plotGenesDetected | Plot genes detected |
| plotGenesPerCell | Plot genes per cell |
| plotGSEATable | Plot GSEA enrichment table |
| plotHeatmap | Heatmap |
| plotIntergenicMappingRate | Plot intergenic mapping rate |
| plotIntronicMappingRate | Plot intronic mapping rate |
| plotKnownMarkers | Plot known markers |
| plotMappedReads | Plot mapped reads |
| plotMappingRate | Plot mapping rate |
| plotMarker | Plot cell-type-specific gene markers |
| plotMeanSD | Plot row standard deviations vs. row means |
| plotMitoRatio | Plot mitochondrial transcript abundance |
| plotMitoVsCoding | Plot mitochondrial vs. coding counts |
| plotNovelty | Plot novelty score |
| plotPCACovariates | Find correlation between principal components (PCs) and covariates |
| plotPCElbow | Plot principal component elbow |
| plotQC | Quality control |
| plotQuantileHeatmap | Quantile heatmap |
| plotReadsPerCell | Plot read counts per cell |
| plotReducedDim | Plot reduced dimensions |
| plotRRNAMappingRate | Plot ribosomal RNA (rRNA) mapping rate |
| plotTopMarkers | Plot top markers |
| plotTotalCounts | Plot total read counts |
| plotTotalReads | Plot total reads |
| plotTSNE | t-SNE plot |
| plotUMAP | UMAP plot |
| plotUMIsPerCell | Plot UMIs per cell |
| plotUMIsVsGenes | Plot UMI and gene correlation |
| plotViolin | Violin plot |
| plotVolcano | Volcano plot |
| plotZerosVsDepth | Plot percentage of zeros vs. library depth |
| pseudobulk | Pseudobulk |
| rankedList | Ranked list |
| relativeLogExpression | Relative log expression |
| removeNA | Remove rows and columns containing only NA values |
| results | Results |
| resultsMatrix | Results matrix |
| resultsNames | Results names |
| resultsTables | Results tables |
| sampleData | Sample data |
| sampleData<- | Sample data |
| sanitizeNA | Sanitize NA values |
| sanitizePercent | Sanitize percentage |
| selectSamples | Select samples |
| snake | Snake case |
| stripTranscriptVersions | Strip transcript versions |
| subsetPerSample | Subset per sample |
| tmm | Trimmed mean of M-values |
| topCellsPerSample | Top cells per sample |
| topMarkers | Top markers |
| topTables | Top tables |
| uniteInterestingGroups | Unite interesting groups into a single column |
| upperCamel | Upper camel case |
| zerosVsDepth | Percentage of zeros vs. library depth |