S4 classes

EggNOG()

EggNOG database annotations

Ensembl2Entrez()

Ensembl-to-Entrez gene identifier mappings

Gene2Symbol()

Gene-to-symbol mappings

HGNC2Ensembl()

HGNC-to-Ensembl gene identifier mappings

MGI2Ensembl()

MGI-to-Ensembl gene identifier mappings

PANTHER()

PANTHER database annotations

Tx2Gene()

Transcript-to-gene identifier mappings

show(<EggNOG>) show(<PANTHER>)

Show an object

summary(<Gene2Symbol>) summary(<Tx2Gene>)

Object summaries

Genome annotations

geneSynonyms()

Gene synonyms

makeGene2SymbolFromEnsembl() makeGene2SymbolFromEnsDb() makeGene2SymbolFromGFF()

Make a Gene2Symbol object

makeTx2GeneFromEnsembl() makeTx2GeneFromEnsDb() makeTx2GeneFromGFF()

Make a Tx2Gene object

matchEnsemblReleaseToURL()

Match Ensembl release to archive URL.

Gene identifier mapping

convertGenesToSymbols() convertSymbolsToGenes()

Convert genes to symbols

convertSampleIDsToNames()

Convert sample identifiers to names

convertTranscriptsToGenes()

Convert transcripts to genes

mapGenesToRownames() mapGenesToIDs() mapGenesToSymbols()

Map genes

matchHumanOrthologs()

Match human gene orthologs

Counts

counts() `counts<-`()

Counts

meltCounts()

Melt count matrix into long format

tpm(<SummarizedExperiment>)

Transcripts per million

Metadata

alphaThreshold() `alphaThreshold<-`()

Alpha threshold

interestingGroups() `interestingGroups<-`()

Interesting groups

lfcThreshold() `lfcThreshold<-`()

Log2 fold change threshold

mcolnames() `mcolnames<-`()

Metadata column names

organism()

Organism

uniteInterestingGroups()

Unite interesting groups into a single column

Sample-level metadata

makeSampleData()

Make sample data

makeSummarizedExperiment()

Make a SummarizedExperiment object

metrics() metricsPerSample()

Quality control metrics

minimalSampleData()

Minimal sample data

sampleData() `sampleData<-`() sampleNames(<SummarizedExperiment>)

Sample data

sampleNames() `sampleNames<-`()

Sample names

selectSamples()

Select samples

Cell-level metadata

aggregateCellsToSamples()

Aggregate cells to samples

cell2sample()

Cell-to-sample mappings

makeSingleCellExperiment()

Make a SingleCellExperiment object

mapCellsToSamples()

Map cells to samples

subsetPerSample()

Subset per sample

topCellsPerSample()

Top cells per sample

Sanitization

autopadZeros()

Autopad zeros

collapseToString()

Collapse to string

relevelRowRanges() relevelColData()

Relevel row or column data

sanitizeSampleData()

Sanitize sample data

sortUnique()

Sort and make unique

stripTranscriptVersions()

Strip transcript versions

toStringUnique()

Convert to a unique character string

Aggregation

aggregateCols() aggregateRows()

Aggregate rows or columns

aggregateCellsToSamples()

Aggregate cells to samples

combine()

Combining or merging different Bioconductor data structures

Math

geometricMean()

Geometric mean

foldChangeToLogRatio() logRatioToFoldChange()

Interconvert log ratio and fold change values

rankedMatrix()

Calculate a ranked matrix

zerosVsDepth()

Percentage of zeros vs. library depth

Markdown

markdown()

Markdown

markdownHeader()

Markdown header

markdownLink()

Markdown hyperlink

markdownList()

Markdown list

markdownPlots()

Multiple Markdown plots

markdownTables()

Multiple Markdown tables

prepareTemplate()

Prepare R Markdown template

Developer

formalsList

Shared list of optional default formals

matchInterestingGroups()

Match interesting groups

multiassignAsEnvir()

Assign multiple objects into a new environment

showHeader()

Header for object show method

showSlotInfo()

Show slot information

Miscellaneous

detectHPC()

Detect HPC environment

detectLanes()

Detect sequencing lanes

geneNames()

Gene names

headtail()

Return the first and last parts of an object

humanize()

Humanize an R object

matchesGene2Symbol()

Check that user-defined gene input matches expected values

matchesInterestingGroups()

Check that interesting groups match a defined value

microplate()

Microtiter plate well identifiers

separator()

Separator bar

Global variables

barcodePattern

Single-sell barcode pattern

genomeMetadataNames

Slot names in metadata containing genome information

lanePattern

Sequencing lane grep pattern

metadataBlacklist

Sample metadata blacklist

Reexports

reexports

Objects exported from other packages