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All functions

Ensembl2Entrez() Entrez2Ensembl()
Ensembl-to-Entrez gene identifier mappings
Gene2Symbol()
Gene-to-symbol mappings
Tx2Gene()
Transcript-to-gene mappings
aggregate() aggregateCols() aggregateRows()
Aggregate
as.SummarizedExperiment()
Coerce to SummarizedExperiment.
autopadZeros()
Autopad zeros
calculateMetrics()
Calculate quality control metrics
combine()
Combine multiple objects
convertGenesToSymbols() convertSymbolsToGenes()
Convert genes to symbols
convertSampleIDsToNames()
Convert sample identifiers to names
convertTranscriptsToGenes()
Convert transcripts to genes
correlation()
Correlation
counts() `counts<-`()
Counts
decode()
Decode column data that uses run-length encoding
detectLanes()
Detect sequencing lanes
droplevels2()
Drop unused levels from factors
encode()
Encode using run-length encoding
estimateSizeFactors()
Estimate size factors
export()
Export
geneNames()
Gene names
headtail()
Return the first and last parts of an object
humanize()
Humanize an R object
importSampleData()
Import sample metadata
integerCounts()
Integer counts
interestingGroups interestingGroups<- interestingGroups,Annotated-method interestingGroups<-,Annotated,NULL-method interestingGroups<-,Annotated,character-method interestingGroups<-,SummarizedExperiment,character-method
Interesting groups
makeSampleData()
Make sample data
makeSummarizedExperiment()
Make a SummarizedExperiment object
mapGenesToRownames() mapGenesToIDs() mapGenesToSymbols()
Map genes
matchInterestingGroups()
Match interesting groups
matchSampleColumn()
Match sample identifier column
melt()
Melt data from wide to long format
metrics()
Quality control metrics
microplate()
Microtiter plate well identifiers
minimalSampleData()
Minimal sample data
nonzeroRowsAndCols()
Subset object to keep only non-zero rows and columns
organism()
Organism
sampleData() `sampleData<-`() sampleNames(<SummarizedExperiment>)
Sample data
sampleNames() `sampleNames<-`()
Sample names
sanitizeSampleData()
Sanitize sample data
selectSamples()
Select samples
sizeFactors() `sizeFactors<-`()
Size factors
stripGeneVersions()
Strip gene identifier versions
stripTranscriptVersions()
Strip transcript identifier versions
camelCase() dottedCase() snakeCase() upperCamelCase()
Syntactic naming functions
tpm()
Transcripts per million
uniteInterestingGroups()
Unite interesting groups into a single column