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All functions

Ensembl2Entrez()
Ensembl-to-Entrez gene identifier mappings
Entrez2Ensembl()
Entrez-to-Ensembl gene identifier mappings
Gene2Symbol()
Gene-to-symbol mappings
KnownMarkers()
Known cell markers
Tx2Gene()
Transcript-to-gene mappings
aggregateCellsToSamples()
Aggregate cells to samples
aggregateCols()
Aggregate columns
aggregateRows()
Aggregate rows
alphaSummary()
Alpha level cutoff summary statistics
alphaThreshold() `alphaThreshold<-`()
Alpha threshold
as.DESeqDataSet()
Coerce object to DESeqDataSet
as.DESeqTransform()
Coerce object to DESeqTransform
as.DGEList()
Coerce object to DGEList
as.DataFrame()
Coerce object to S4 DataFrame
as.Seurat()
Coerce object to Seurat
as.SingleCellExperiment()
Coerce object to SingleCellExperiment
as.SummarizedExperiment()
Coerce object to SummarizedExperiment
atomize()
Atomize
autopadZeros()
Autopad zeros
barcodeRanksPerSample()
Barcode ranks per sample
baseMeanThreshold() `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
coerceToList()
Coerce to list
collapseToString()
Collapse to string
collectionNames() `collectionNames<-`()
Gene set collection names
contrastName() `contrastName<-`()
Contrast name
contrastNames() `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
cpm()
Counts per million
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
droplevels2()
Drop factor levels
encode()
Encode using run-length encoding
enrichedGeneSets()
Enriched gene sets
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
geneIDs()
Gene identifiers
geneNames()
Gene names
geneSet()
Gene set
geneSetNames()
Gene set names
geneSetResults()
Gene set results
geometricMean()
Geometric mean
headtail()
Return the first and last parts of an object
humanize()
Humanize an R object
integerCounts()
Integer counts
interestingGroups() `interestingGroups<-`()
Interesting groups
intersectAll()
Intersection of more than two vectors
intersectionMatrix()
Intersection matrix
innerJoin() leftJoin() rightJoin() fullJoin() semiJoin() antiJoin()
Join operations
kebabCase()
Kebab case
leadingEdge()
Leading edge genes
lfcShrink() `lfcShrink<-`()
Shrink log2 fold changes
lfcShrinkType()
Shrunken log2 fold change (LFC) type
lfcThreshold() `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() `metadata2<-`()
Metadata
metrics()
Quality control metrics
metricsPerSample()
Quality control metrics per sample
mutateAll() mutateAt() mutateIf() transmuteAt() transmuteIf()
Mutate multiple columns
nesThreshold() `nesThreshold<-`()
Normalized enrichment score (NES) threshold
nonzeroRowsAndCols()
Subset object to keep only non-zero rows and columns
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
plotCellTypesPerCluster()
Plot cell types per cluster
plotCells()
Plot cells
plotContrastScatter()
Plot scatterplot of differential expression contrast
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
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
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
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
plotRRNAMappingRate()
Plot ribosomal RNA (rRNA) mapping rate
plotReadsPerCell()
Plot read counts per cell
plotReducedDim()
Plot reduced dimensions
plotStackedBarPlot()
Plot stacked bar plot
plotSums()
Plot row or column sums
plotTSNE()
t-SNE plot
plotTopMarkers()
Plot top markers
plotTotalCounts()
Plot total read counts
plotTotalReads()
Plot total reads
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() `resultsNames<-`()
Results names
resultsTables()
Results tables
sampleData() `sampleData<-`()
Sample data
sanitizeNA()
Sanitize NA values
sanitizePercent()
Sanitize percentage
selectIf()
Select multiple columns
selectSamples()
Select samples
sem()
Standard error of the mean
sentenceCase()
Sentence case
showHeader()
Header for object show method
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
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
uniteInterestingGroups()
Unite interesting groups into a single column
upperCamelCase()
Upper camel case
zerosVsDepth()
Percentage of zeros vs. library depth