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

emptyRanges()

Generate empty genomic ranges

geneSynonyms()

Gene synonyms

makeGRangesFromEnsDb()

Make GRanges from EnsDb object

makeGRangesFromEnsembl() annotable()

Make GRanges from Ensembl

makeGRangesFromGFF() makeGRangesFromGTF()

Make GRanges from a GFF/GTF file

makeGene2SymbolFromEnsembl() makeGene2SymbolFromEnsDb() makeGene2SymbolFromGFF()

Make a Gene2Symbol object

makeTx2GeneFromEnsembl() makeTx2GeneFromEnsDb() makeTx2GeneFromGFF()

Make a Tx2Gene object

Gene identifier mapping

convertGenesToSymbols(<character>) convertGenesToSymbols(<matrix>) convertGenesToSymbols(<sparseMatrix>) convertGenesToSymbols(<SummarizedExperiment>) convertSymbolsToGenes(<SummarizedExperiment>)

Convert genes to symbols

convertSampleIDsToNames(<SummarizedExperiment>) convertSampleIDsToNames(<SingleCellExperiment>)

Convert sample identifiers to names

convertTranscriptsToGenes(<character>) convertTranscriptsToGenes(<matrix>) convertTranscriptsToGenes(<sparseMatrix>) convertTranscriptsToGenes(<SummarizedExperiment>)

Convert transcripts to genes

convertUCSCBuildToEnsembl()

Convert UCSC build to Ensembl

mapGenesToRownames(<Gene2Symbol>) mapGenesToRownames(<SummarizedExperiment>) mapGenesToIDs(<Gene2Symbol>) mapGenesToIDs(<SummarizedExperiment>) mapGenesToSymbols(<Gene2Symbol>) mapGenesToSymbols(<SummarizedExperiment>)

Map genes

Counts

counts(<SummarizedExperiment>) `counts<-`(<SummarizedExperiment>)

Counts

meltCounts(<SummarizedExperiment>)

Melt count matrix into long format

tpm(<SummarizedExperiment>)

Transcripts per million

Metadata

interestingGroups(<SummarizedExperiment>) `interestingGroups<-`(<SummarizedExperiment>,<character>) `interestingGroups<-`(<SummarizedExperiment>,<NULL>)

Interesting groups

organism(<matrix>) organism(<sparseMatrix>) organism(<data.frame>) organism(<DataFrame>) organism(<GRanges>) organism(<SummarizedExperiment>)

Organism

uniteInterestingGroups(<DataFrame>)

Unite interesting groups into a single column

Sample-level metadata

makeSampleData()

Make sample data

makeSummarizedExperiment()

Make a SummarizedExperiment object

metrics(<SummarizedExperiment>) metrics(<SingleCellExperiment>) metricsPerSample(<SingleCellExperiment>)

Quality control metrics

minimalSampleData()

Minimal sample data

sampleData(<SummarizedExperiment>) sampleData(<SingleCellExperiment>) `sampleData<-`(<SummarizedExperiment>,<DataFrame>) `sampleData<-`(<SingleCellExperiment>,<DataFrame>) sampleNames(<SummarizedExperiment>)

Sample data

`sampleNames<-`(<SummarizedExperiment>,<character>)

Sample names

selectSamples(<SummarizedExperiment>) selectSamples(<SingleCellExperiment>)

Select samples

Cell-level metadata

aggregateCellsToSamples(<SingleCellExperiment>)

Aggregate cells to samples

cell2sample(<SingleCellExperiment>)

Cell-to-sample mappings

makeSingleCellExperiment()

Make a SingleCellExperiment object

mapCellsToSamples()

Map cells to samples

subsetPerSample(<SingleCellExperiment>)

Subset per sample

topCellsPerSample(<SingleCellExperiment>)

Top cells per sample

Sanitization

autopadZeros(<character>) autopadZeros(<matrix>) autopadZeros(<SummarizedExperiment>)

Autopad zeros

collapseToString(<atomic>) collapseToString(<matrix>) collapseToString(<data.frame>) collapseToString(<DataFrame>)

Collapse to string

relevelRowRanges() relevelColData()

Relevel row or column data

removeNA(<atomic>) removeNA(<matrix>) removeNA(<sparseMatrix>) removeNA(<data.frame>) removeNA(<DataFrame>)

Remove rows and columns containing only NA values

sanitizeNA(<atomic>) sanitizeNA(<character>) sanitizeNA(<factor>) sanitizeNA(<data.frame>) sanitizeNA(<DataFrame>)

Sanitize NA values

sanitizePercent(<atomic>) sanitizePercent(<character>)

Sanitize percentage

sanitizeSampleData()

Sanitize sample data

sortUnique()

Sort and make unique

stripTranscriptVersions(<character>) stripTranscriptVersions(<matrix>) stripTranscriptVersions(<sparseMatrix>) stripTranscriptVersions(<SummarizedExperiment>)

Strip transcript versions

toStringUnique()

Convert to a unique character string

Aggregation

aggregateRows(<matrix>) aggregateRows(<sparseMatrix>) aggregateRows(<SummarizedExperiment>) aggregateCols(<matrix>) aggregateCols(<sparseMatrix>) aggregateCols(<SummarizedExperiment>) aggregateCols(<SingleCellExperiment>)

Aggregate rows or columns

aggregateCellsToSamples(<SingleCellExperiment>)

Aggregate cells to samples

combine(<SummarizedExperiment>,<SummarizedExperiment>) combine(<SingleCellExperiment>,<SingleCellExperiment>)

Combining or merging different Bioconductor data structures

Math

geometricMean(<numeric>) geometricMean(<matrix>) geometricMean(<sparseMatrix>)

Geometric mean

foldChangeToLogRatio(<numeric>) logRatioToFoldChange(<numeric>)

Interconvert log ratio and fold change values

zerosVsDepth(<matrix>) zerosVsDepth(<sparseMatrix>) zerosVsDepth(<SummarizedExperiment>) zerosVsDepth(<SingleCellExperiment>)

Percentage of zeros vs. library depth

Plots

plotCorrelationHeatmap(<SummarizedExperiment>) plotCorrelationHeatmap(<SingleCellExperiment>)

Correlation heatmap

plotCounts(<SummarizedExperiment>)

Plot counts

plotCountsPerBiotype(<SummarizedExperiment>) plotCountsPerBroadClass(<SummarizedExperiment>)

Plot counts per biotype

plotCountsPerBroadClass

Plot counts per broad class definition

plotCountsPerGene(<SummarizedExperiment>) plotCountsPerGene(<SingleCellExperiment>)

Plot counts per gene

plotGenderMarkers(<SummarizedExperiment>)

Plot sexually dimorphic gender marker genes

plotGenesDetected(<SummarizedExperiment>) plotGenesDetected(<SingleCellExperiment>)

Plot genes detected

plotHeatmap(<SummarizedExperiment>) plotHeatmap(<SingleCellExperiment>)

Heatmap

plotPCA(<SummarizedExperiment>)

Principal component analysis plot

plotQC(<SummarizedExperiment>)

Quality control

plotQuantileHeatmap(<SummarizedExperiment>) plotQuantileHeatmap(<SingleCellExperiment>)

Quantile heatmap

plotTotalCounts(<SummarizedExperiment>) plotTotalCounts(<SingleCellExperiment>)

Plot total read counts

plotZerosVsDepth(<SummarizedExperiment>)

Plot percentage of zeros vs. library depth

ggplot2

basejump_geom_abline() basejump_geom_label() basejump_geom_label_average() basejump_geom_label_repel()

ggplot2 geometric objects

theme_paperwhite() theme_midnight()

ggplot2 themes

Markdown

markdown(<SummarizedExperiment>)

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

showSlotInfo()

Show slot information

Miscellaneous

detectHPC()

Detect HPC environment

detectLanes()

Detect sequencing lanes

detectOrganism()

Detect organism

geneNames(<GRanges>) geneNames(<SummarizedExperiment>)

Gene names

headtail(<atomic>) headtail(<matrix>) headtail(<sparseMatrix>) headtail(<data.frame>) headtail(<DataFrame>) headtail(<GRanges>) headtail(<SummarizedExperiment>)

Return the first and last parts of an object

humanize(<SummarizedExperiment>)

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

Example data

df

Example DataFrame

gender_markers

Sexually dimorphic gender marker genes

mat

Example matrix

organism_mappings

Organism mappings

rse

Example SummarizedExperiment

sce

Example SingleCellExperiment

sparse

Example sparseMatrix

tbl

Example tibble (tbl_df)

tx_se

Example transcript-level SummarizedExperiment