AcidExperiment-package | AcidExperiment |
AcidExperimentTestsURL | AcidExperiment test data URL |
aggregate | Aggregate |
as.SummarizedExperiment | Coerce to 'SummarizedExperiment'. |
autopadZeros | Autopad zeros |
calculateMetrics | Calculate quality control metrics |
combine | Combine multiple objects |
convertGenesToSymbols | Convert genes to symbols |
convertSampleIDsToNames | Convert sample identifiers to names |
convertTranscriptsToGenes | Convert transcripts to genes |
correlation | Correlation |
counts | Counts |
decode | Decode column data that uses run-length encoding |
defunct | Defunct functions |
detectLanes | Detect sequencing lanes |
droplevels2 | Drop unused levels from factors |
encode | Encode using run-length encoding |
Ensembl2Entrez | Ensembl-to-Entrez gene identifier mappings |
estimateSizeFactors | Estimate size factors |
export | Export |
Gene2Symbol | Gene-to-symbol mappings |
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 | Interesting groups |
makeSampleData | Make sample data |
makeSummarizedExperiment | Make a SummarizedExperiment object |
mapGenes | Map genes |
matchInterestingGroups | Match interesting groups |
matchSampleColumn | Match sample identifier column |
melt | Melt columns into key-value pairs |
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 | Sample data |
sampleNames | Sample names |
sanitizeSampleData | Sanitize sample data |
selectSamples | Select samples |
sizeFactors | Size factors |
stripGeneVersions | Strip gene identifier versions |
stripTranscriptVersions | Strip transcript identifier versions |
syntactic | Syntactic naming functions |
tpm | Transcripts per million |
Tx2Gene | Transcript-to-gene mappings |
uniteInterestingGroups | Unite interesting groups into a single column |
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