A B C D E F G H I L M N O P R S T U W Z
aggregate | Aggregate rows or columns |
aggregateCellsToSamples | Aggregate cells to samples |
aggregateCellsToSamples-method | Aggregate cells to samples |
aggregateCols | Aggregate rows or columns |
aggregateCols-method | Aggregate rows or columns |
aggregateRows | Aggregate rows or columns |
aggregateRows-method | Aggregate rows or columns |
alphaThreshold | Alpha threshold |
alphaThreshold-method | Alpha threshold |
alphaThreshold<- | Alpha threshold |
alphaThreshold<--method | Alpha threshold |
autopadZeros | Autopad zeros |
autopadZeros-method | Autopad zeros |
barcodePattern | Single-sell barcode pattern |
calculateMetrics | Calculate quality control metrics |
calculateMetrics-method | Calculate quality control metrics |
camelCase | Camel case |
camelCase-method | Camel case |
cell2sample | Cell-to-sample mappings |
cell2sample-method | Cell-to-sample mappings |
collapseToString | Collapse to string |
collapseToString-method | Collapse to string |
combine | Combining or merging different Bioconductor data structures |
combine-method | Combining or merging different Bioconductor data structures |
convertGenesToSymbols | Convert genes to symbols |
convertGenesToSymbols-method | Convert genes to symbols |
convertSampleIDsToNames | Convert sample identifiers to names |
convertSampleIDsToNames-method | Convert sample identifiers to names |
convertSymbolsToGenes | Convert genes to symbols |
convertSymbolsToGenes-method | Convert genes to symbols |
convertTranscriptsToGenes | Convert transcripts to genes |
convertTranscriptsToGenes-method | Convert transcripts to genes |
correlation | Correlation |
correlation-method | Correlation |
counts | Counts |
counts-method | Counts |
counts<- | Counts |
counts<--method | Counts |
detectHPC | Detect HPC environment |
detectLanes | Detect sequencing lanes |
dottedCase | Dotted case |
dottedCase-method | Dotted case |
Ensembl2Entrez | Ensembl-to-Entrez gene identifier mappings |
Ensembl2Entrez-class | Ensembl-to-Entrez gene identifier mappings |
Ensembl2Entrez-method | Ensembl-to-Entrez gene identifier mappings |
ensemblVersion | Genome versions |
estimateSizeFactors | Estimate size factors |
estimateSizeFactors-method | Estimate size factors |
filterCells | Filter cells |
filterCells-method | Filter cells |
flybaseVersion | Genome versions |
foldChangeToLogRatio | Interconvert log ratio and fold change values |
foldChangeToLogRatio-method | Interconvert log ratio and fold change values |
formalsList | Shared list of optional default formals |
gencodeVersion | Genome versions |
Gene2Symbol | Gene-to-symbol mappings |
Gene2Symbol-class | Gene-to-symbol mappings |
Gene2Symbol-method | Gene-to-symbol mappings |
geneNames | Gene names |
geneNames-method | Gene names |
geneSynonyms | Gene synonyms |
genomeMetadataNames | Slot names in metadata containing genome information |
genomeVersions | Genome versions |
geometricMean | Geometric mean |
geometricMean-method | Geometric mean |
headtail | Return the first and last parts of an object |
headtail-method | Return the first and last parts of an object |
HGNC2Ensembl | HGNC-to-Ensembl gene identifier mappings |
HGNC2Ensembl-class | HGNC-to-Ensembl gene identifier mappings |
humanize | Humanize an R object |
humanize-method | Humanize an R object |
importSampleData | Import sample metadata |
importTx2Gene | Import transcript-to-gene annotations |
interestingGroups | Interesting groups |
interestingGroups-method | Interesting groups |
interestingGroups<- | Interesting groups |
interestingGroups<--method | Interesting groups |
lanePattern | Sequencing lane grep pattern |
lfcThreshold | Log2 fold change threshold |
lfcThreshold-method | Log2 fold change threshold |
lfcThreshold<- | Log2 fold change threshold |
lfcThreshold<--method | Log2 fold change threshold |
logRatio | Interconvert log ratio and fold change values |
logRatioToFoldChange | Interconvert log ratio and fold change values |
logRatioToFoldChange-method | Interconvert log ratio and fold change values |
makeGene2Symbol | Make a Gene2Symbol object |
makeGene2SymbolFromEnsDb | Make a Gene2Symbol object |
makeGene2SymbolFromEnsembl | Make a Gene2Symbol object |
makeGene2SymbolFromGFF | Make a Gene2Symbol object |
makeGene2SymbolFromGTF | Make a Gene2Symbol object |
makeSampleData | Make sample data |
makeSampleData-method | Make sample data |
makeSingleCellExperiment | Make a SingleCellExperiment object |
makeSingleCellExperiment-method | Make a SingleCellExperiment object |
makeSummarizedExperiment | Make a SummarizedExperiment object |
makeSummarizedExperiment-method | Make a SummarizedExperiment object |
makeTx2Gene | Make a Tx2Gene object |
makeTx2GeneFromEnsDb | Make a Tx2Gene object |
makeTx2GeneFromEnsembl | Make a Tx2Gene object |
makeTx2GeneFromFASTA | Make a Tx2Gene object from transcriptome FASTA |
makeTx2GeneFromGFF | Make a Tx2Gene object |
makeTx2GeneFromGTF | Make a Tx2Gene object |
mapCellsToSamples | Map cells to samples |
mapGenes | Map genes |
mapGenesToIDs | Map genes |
mapGenesToIDs-method | Map genes |
mapGenesToRownames | Map genes |
mapGenesToRownames-method | Map genes |
mapGenesToSymbols | Map genes |
mapGenesToSymbols-method | Map genes |
markdown | Markdown |
markdown-method | Markdown |
markdownHeader | Markdown header |
markdownLink | Markdown hyperlink |
markdownList | Markdown list |
markdownPlots | Multiple Markdown plots |
markdownTables | Multiple Markdown tables |
matchEnsemblReleaseToURL | Match Ensembl release to archive URL. |
matchesGene2Symbol | Check that user-defined gene input matches expected values |
matchesInterestingGroups | Check that interesting groups match a defined value |
matchHumanOrthologs | Match human gene orthologs |
matchInterestingGroups | Match interesting groups |
mcolnames | Metadata column names |
mcolnames-method | Metadata column names |
mcolnames<- | Metadata column names |
mcolnames<--method | Metadata column names |
mdHeader | Markdown header |
mdLink | Markdown hyperlink |
mdList | Markdown list |
mdPlots | Multiple Markdown plots |
mdTables | Multiple Markdown tables |
melt | Melt columns into key-value pairs |
melt-method | Melt columns into key-value pairs |
metadataBlacklist | Sample metadata blacklist |
metrics | Quality control metrics |
metrics-method | Quality control metrics |
metricsCols | Quality control metric columns |
metricsPerSample | Quality control metrics |
metricsPerSample-method | Quality control metrics |
MGI2Ensembl | MGI-to-Ensembl gene identifier mappings |
MGI2Ensembl-class | MGI-to-Ensembl gene identifier mappings |
microplate | Microtiter plate well identifiers |
minimalSampleData | Minimal sample data |
multiassignAsEnvir | Assign multiple objects into a new environment |
nonzeroRowsAndCols | Subset object to keep only non-zero rows and columns |
nonzeroRowsAndCols-method | Subset object to keep only non-zero rows and columns |
organism | Organism |
organism-method | Organism |
organism<- | Organism |
organism<--method | Organism |
prepareTemplate | Prepare R Markdown template |
pseudobulk | Pseudobulk |
pseudobulk-method | Pseudobulk |
rankedMatrix | Calculate a ranked matrix |
refseqVersion | Genome versions |
sampleData | Sample data |
sampleData-method | Sample data |
sampleData<- | Sample data |
sampleData<--method | Sample data |
sampleNames | Sample names |
sampleNames-method | Sample data |
sampleNames<- | Sample names |
sampleNames<--method | Sample names |
sanitizeSampleData | Sanitize sample data |
selectSamples | Select samples |
selectSamples-method | Select samples |
separator | Separator bar |
showHeader | Header for object show method |
showSlotInfo | Show slot information |
sizeFactors | Size factors |
sizeFactors-method | Size factors |
sizeFactors<- | Size factors |
sizeFactors<--method | Size factors |
snakeCase | Snake case |
snakeCase-method | Snake case |
sortUnique | Sort and make unique |
stripGeneVersions | Strip transcript versions |
stripTranscriptVersions | Strip transcript versions |
stripTranscriptVersions-method | Strip transcript versions |
subsetPerSample | Subset per sample |
subsetPerSample-method | Subset per sample |
topCellsPerSample | Top cells per sample |
topCellsPerSample-method | Top cells per sample |
toStringUnique | Convert to a unique character string |
tpm | Transcripts per million |
tpm-method | Transcripts per million |
Tx2Gene | Transcript-to-gene identifier mappings |
Tx2Gene-class | Transcript-to-gene identifier mappings |
Tx2Gene-method | Transcript-to-gene identifier mappings |
uniteInterestingGroups | Unite interesting groups into a single column |
uniteInterestingGroups-method | Unite interesting groups into a single column |
upperCamelCase | Upper camel case |
upperCamelCase-method | Upper camel case |
wormbaseVersion | Genome versions |
zerosVsDepth | Percentage of zeros vs. library depth |
zerosVsDepth-method | Percentage of zeros vs. library depth |