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A B C D E F G H I J K L M N O P R S T U Z
| aggregate | Aggregate |
| aggregateCellsToSamples | Aggregate cells to samples |
| aggregateCols | Aggregate columns |
| aggregateRows | Aggregate rows |
| alphaSummary | Alpha level cutoff summary statistics |
| alphaThreshold | Alpha threshold |
| alphaThreshold<- | Alpha threshold |
| antiJoin | Join operations |
| as.data.frame | Coerce object to a data frame |
| as.DataFrame | Coerce object to S4 DataFrame |
| as.DESeqDataSet | Coerce object to 'DESeqDataSet' |
| as.DESeqTransform | Coerce object to 'DESeqTransform' |
| as.DGEList | Coerce object to 'DGEList' |
| as.list | Coerce object to a list |
| as.SummarizedExperiment | Coerce object to SummarizedExperiment |
| atomize | Atomize |
| autopadZeros | Autopad zeros |
| barcodeRanksPerSample | Barcode ranks per sample |
| baseMeanThreshold | Base mean threshold |
| baseMeanThreshold<- | Base mean threshold |
| calculateMetrics | Calculate quality control metrics |
| camelCase | Camel case |
| capitalize | Capitalize |
| cell2sample | Cell-to-sample mappings |
| cellCountsPerCluster | Cell counts per cluster |
| cellTypesPerCluster | Cell types per cluster |
| clusters | Cluster identifiers |
| coerce | Coerce an object to a class |
| coerceToList | Coerce to list |
| collapseToString | Collapse to string |
| collectionNames | Gene set collection names |
| collectionNames<- | Gene set collection names |
| combine | Combine multiple objects |
| contrastName | Contrast name |
| 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 |
| convertToHuman | Convert data set by mapping to human orthologs |
| convertTranscriptsToGenes | Convert transcripts to genes |
| correlation | Correlation |
| counts | Counts |
| counts<- | Counts |
| cpm | Counts per million |
| decode | Decode (run-length encoding) |
| deg | Differentially expressed genes |
| degIntersection | Intersection of differentially expressed genes |
| degPerContrast | Differentially expressed genes per contrast |
| diffExp | Differential expression |
| diffExpPerCluster | Differential expression per cluster |
| dottedCase | Dotted case |
| droplevels | Drop levels |
| encode | Encode using run-length encoding |
| enrichedGeneSets | Enriched gene sets |
| estimateSizeFactors | Estimate size factors |
| export | Export |
| factorize | Factorize |
| filterCells | Filter cells |
| findMarkers | Find cluster-specific marker genes |
| foldChangeToLogRatio | Fold change to log ratio |
| fpkm | Fragments per kilobase per million mapped fragments |
| fullJoin | Join operations |
| geneIDs | Gene identifiers |
| geneNames | Gene names |
| geneSet | Gene set |
| geneSetNames | Gene set names |
| geneSetResults | Gene set results |
| geometricMean | Geometric mean |
| head | Return the first part of an object |
| headtail | Return the first and last parts of an object |
| humanize | Humanize an R object |
| innerJoin | Join operations |
| integerCounts | Integer counts |
| interestingGroups | Interesting groups |
| interestingGroups<- | Interesting groups |
| intersectAll | Intersection of more than two vectors |
| intersectionMatrix | Intersection matrix |
| join | Join operations |
| kebabCase | Kebab case |
| leadingEdge | Leading edge genes |
| leftJoin | Join operations |
| lfcShrink | Shrink log2 fold changes |
| lfcShrink<- | Shrink log2 fold changes |
| lfcShrinkType | Shrunken log2 fold change (LFC) type |
| lfcThreshold | Log2 fold change threshold |
| lfcThreshold<- | Log2 fold change threshold |
| logRatioToFoldChange | Log ratio to fold change |
| makeDimnames | Make syntactically valid dimnames |
| makeLabel | Make a plot axis or legend label out of a character string |
| makeNames | Make syntactically valid names |
| makeSampleData | Make sample data |
| makeTitle | Make a title out of character string |
| makeWords | Convert syntactic names to words separated by spaces |
| mapCells | Map input to cell identifiers |
| mapColnames | Map input to column names |
| mapGenes | Map input to gene identifiers |
| mapGenesToIDs | Map genes (gene names) to gene identifiers |
| mapGenesToRownames | Map genes to row names |
| mapGenesToSymbols | Map genes (gene identifiers) to gene names (symbols) |
| mapRownames | Map input to row names |
| mapToDataFrame | Map elements to a data frame by row binding |
| matchCellColumn | Match cell identifier column |
| matchGeneColumn | Match gene identifier column |
| matchRownameColumn | Match row name column |
| matchSampleColumn | Match sample identifier column |
| matchTranscriptColumn | Match transcript identifier column |
| melt | Melt columns into key-value pairs |
| metadata2 | Metadata |
| metadata2<- | Metadata |
| metrics | Quality control metrics |
| metricsPerSample | Quality control metrics per sample |
| missingOrNULL-class | Missing or NULL class union |
| mutate | Mutate multiple columns |
| mutateAll | Mutate multiple columns |
| mutateAt | Mutate multiple columns |
| mutateIf | Mutate multiple columns |
| nesThreshold | Normalized enrichment score (NES) threshold |
| nesThreshold<- | Normalized enrichment score (NES) threshold |
| nonzeroRowsAndCols | Subset object to keep only non-zero rows and columns |
| normalize | Normalize an object |
| organism | Organism |
| organism<- | Organism |
| plot5Prime3PrimeBias | Plot 5' to 3' bias |
| plotBarcodeRanks | Plot barcode ranks |
| plotBaseMean | Plot base mean distribution |
| plotCellCounts | Plot cell counts |
| plotCellCountsPerCluster | Plot cell counts per cluster |
| plotCells | Plot cells |
| plotCellTypesPerCluster | Plot cell types per cluster |
| plotCorrelation | Correlation X-Y scatterplot |
| plotCorrelationHeatmap | Correlation heatmap |
| plotCountDensity | Plot count density |
| plotCounts | Plot counts |
| plotCountsCorrelation | Plot counts correlation |
| plotCountsCorrelationHeatmap | Plot counts correlation heatmap |
| plotCountsPerBiotype | Plot counts per biotype |
| plotCountsPerBroadClass | Plot counts per broad class definition |
| plotCountsPerCell | Plot counts per cell |
| plotCountsPerFeature | Plot counts per feature |
| plotCountsPerGene | Plot counts per gene |
| plotCountsVsFeatures | Plot count and feature correlation |
| plotDEGHeatmap | Differentially expressed gene heatmap |
| plotDEGPCA | Plot differentially expressed gene principal component analysis |
| plotDEGStackedBar | Stacked bar plot of DEGs |
| plotDEGUpset | UpSet plot of directional DEG intersections across contrasts |
| plotDispEsts | Plot dispersion estimates |
| plotDots | 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 |
| plotFeaturesPerCell | Plot features per cell |
| plotGenderMarkers | Plot sexually dimorphic gender marker genes |
| plotGeneSaturation | Plot gene detection saturation |
| plotGeneSet | Plot gene set enrichment |
| plotHeatmap | Heatmap |
| plotIntergenicMappingRate | Plot intergenic mapping rate |
| plotIntronicMappingRate | Plot intronic mapping rate |
| plotKnownMarkers | Plot known markers |
| plotLFC | Plot log2 fold change distributions |
| plotMA | MA plot |
| 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 |
| plotNES | Plot normalized enrichment score |
| plotNovelty | Plot novelty score |
| plotPCA | Principal component analysis plot |
| plotPCACovariates | Find correlation between principal components (PCs) and covariates |
| plotPCElbow | Plot principal component elbow |
| plotPseudoVsAlignedCounts | Plot pseudo vs. aligned counts |
| plotQC | Quality control |
| plotQuantileHeatmap | Quantile heatmap |
| plotReadsPerCell | Plot read counts per cell |
| plotReducedDim | Plot reduced dimensions |
| plotRRNAMappingRate | Plot ribosomal RNA (rRNA) mapping rate |
| plotStackedBarPlot | Plot stacked bar plot |
| plotSums | Plot row or column sums |
| plotTopMarkers | Plot top markers |
| plotTotalCounts | Plot total read counts |
| plotTotalReads | Plot total reads |
| plotTSNE | t-SNE plot |
| plotUMAP | UMAP plot |
| plotUpset | UpSet plot |
| plotViolin | Violin plot |
| plotVolcano | Volcano plot |
| plotWaterfall | Plot waterfall |
| plotZerosVsDepth | Plot percentage of zeros vs. library depth |
| rankedMatrix | Calculate a ranked matrix |
| rbindToDataFrame | Row bind elements 1:1 to a data frame |
| relativeLogExpression | Relative log expression |
| removeNA | Remove rows and columns containing only NA values |
| results | Results |
| resultsDiff | Relative difference of results |
| resultsMatrix | Results matrix |
| resultsNames | Results names |
| resultsNames<- | Results names |
| resultsTables | Results tables |
| rightJoin | Join operations |
| sampleData | Sample data |
| sampleData<- | Sample data |
| sampleNames | Sample names |
| sampleNames<- | Sample names |
| sanitizeNA | Sanitize NA values |
| sanitizePercent | Sanitize percentage |
| select | Select multiple columns |
| selectIf | Select multiple columns |
| selectSamples | Select samples |
| sem | Standard error of the mean |
| semiJoin | Join operations |
| sentenceCase | Sentence case |
| show | Show an object |
| showHeader | Header for object show method |
| sizeFactors | Size factors |
| sizeFactors<- | Size factors |
| slotAlignedCounts | Slot aligned counts |
| snakeCase | Snake case |
| splitByLevel | Split by factor level |
| standardizeCells | Standardize cell line names |
| stripGeneVersions | Strip gene identifier versions |
| stripTranscriptVersions | Strip transcript identifier versions |
| subsetPerSample | Subset per sample |
| summary | Summary |
| tail | Return the last part of an object |
| tmm | Trimmed mean of M-values |
| topCellsPerSample | Top cells per sample |
| topMarkers | Top markers |
| topTables | Top tables |
| tpm | Transcripts per million |
| transcriptIDs | Transcript identifiers |
| transcriptNames | Transcript names |
| transformType | Variance-stabilizing transformation type |
| transmuteAt | Mutate multiple columns |
| transmuteIf | Mutate multiple columns |
| uniteInterestingGroups | Unite interesting groups into a single column |
| updateObject | Update object |
| upperCamelCase | Upper camel case |
| zerosVsDepth | Percentage of zeros vs. library depth |