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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 |