All functions

aggregate()

Aggregate

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.SummarizedExperiment()

Coerce object to SummarizedExperiment

as.data.frame()

Coerce object to a data frame

as.list()

Coerce object to a list

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

coerce()

Coerce an object to a class

coerceToList()

Coerce to list

collapseToString()

Collapse to string

collectionNames() `collectionNames<-`()

Gene set collection names

combine()

Combine multiple objects

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

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

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

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

missingOrNULL-class

Missing or NULL class union

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

normalize()

Normalize an object

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

plotCellTypesPerCluster()

Plot cell types per cluster

plotCells()

Plot cells

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

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

sampleNames() `sampleNames<-`()

Sample names

sanitizeNA()

Sanitize NA values

sanitizePercent()

Sanitize percentage

selectIf()

Select multiple columns

selectSamples()

Select samples

sem()

Standard error of the mean

sentenceCase()

Sentence case

show()

Show an object

showHeader()

Header for object show method

sizeFactors() `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

uniteInterestingGroups()

Unite interesting groups into a single column

updateObject()

Update object

upperCamelCase()

Upper camel case

zerosVsDepth()

Percentage of zeros vs. library depth