![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
A B C D E F G H I L M O P R S T U Z
| aggregate | Aggregate rows or columns |
| aggregateCellsToSamples | Aggregate cells to samples |
| aggregateCellsToSamples-method | Aggregate cells to samples |
| aggregateCols-method | Aggregate rows or columns |
| aggregateRows-method | Aggregate rows or columns |
| annotable | Make a 'GenomicRanges' object |
| autopadZeros | Autopad zeros |
| autopadZeros-method | Autopad zeros |
| barcodePattern | Single-sell barcode pattern |
| basejump_geom_abline | ggplot2 geometric objects |
| basejump_geom_label | ggplot2 geometric objects |
| basejump_geom_label_average | ggplot2 geometric objects |
| basejump_geom_label_repel | ggplot2 geometric objects |
| 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-method | Convert genes to symbols |
| convertTranscriptsToGenes | Convert transcripts to genes |
| convertTranscriptsToGenes-method | Convert transcripts to genes |
| convertUCSCBuildToEnsembl | Convert UCSC build to Ensembl |
| counts | Counts |
| counts-method | Counts |
| counts<- | Counts |
| counts<--method | Counts |
| detectHPC | Detect HPC environment |
| detectLanes | Detect sequencing lanes |
| detectOrganism | Detect organism |
| df | Example 'DataFrame' |
| EggNOG | EggNOG database annotations |
| EggNOG-class | EggNOG database annotations |
| emptyRanges | Generate empty genomic ranges |
| Ensembl2Entrez | Ensembl-to-Entrez gene identifier mappings |
| Ensembl2Entrez-class | Ensembl-to-Entrez gene identifier mappings |
| Ensembl2Entrez-method | Ensembl-to-Entrez gene identifier mappings |
| foldChangeToLogRatio-method | Interconvert log ratio and fold change values |
| formalsList | Shared list of optional default formals |
| gender_markers | Sexually dimorphic gender marker genes |
| 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 |
| geometricMean | Geometric mean |
| geometricMean-method | Geometric mean |
| ggplot2-geoms | ggplot2 geometric objects |
| ggplot2-themes | ggplot2 themes |
| 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 |
| interestingGroups | Interesting groups |
| interestingGroups-method | Interesting groups |
| interestingGroups<--method | Interesting groups |
| lanePattern | Sequencing lane grep pattern |
| logRatio | 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 |
| makeGRanges | Make a 'GenomicRanges' object |
| makeGRangesFromEnsDb | Make a 'GenomicRanges' object |
| makeGRangesFromEnsembl | Make a 'GenomicRanges' object |
| makeGRangesFromGFF | Make a 'GenomicRanges' object |
| makeGRangesFromGTF | Make a 'GenomicRanges' object |
| makeSampleData | Make sample data |
| makeSingleCellExperiment | Make a 'SingleCellExperiment' object |
| makeSummarizedExperiment | Make a 'SummarizedExperiment' object |
| makeTx2Gene | Make a 'Tx2Gene' object |
| makeTx2GeneFromEnsDb | Make a 'Tx2Gene' object |
| makeTx2GeneFromEnsembl | Make a 'Tx2Gene' object |
| makeTx2GeneFromGFF | Make a 'Tx2Gene' object |
| makeTx2GeneFromGTF | Make a 'Tx2Gene' object |
| mapCellsToSamples | Map cells to samples |
| mapGenes | Map genes |
| mapGenesToIDs-method | Map genes |
| mapGenesToRownames-method | 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 |
| mat | Example 'matrix' |
| matchesGene2Symbol | Check that user-defined gene input matches expected values |
| matchesInterestingGroups | Check that interesting groups match a defined value |
| matchInterestingGroups | Match interesting groups |
| mdHeader | Markdown header |
| mdLink | Markdown hyperlink |
| mdList | Markdown list |
| mdPlots | Multiple Markdown plots |
| mdTables | Multiple Markdown tables |
| meltCounts | Melt count matrix into long format |
| meltCounts-method | Melt count matrix into long format |
| metrics | Quality control metrics |
| metrics-method | 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 |
| organism | Organism |
| organism-method | Organism |
| organism_mappings | Organism mappings |
| PANTHER | PANTHER database annotations |
| PANTHER-class | PANTHER database annotations |
| plotCorrelationHeatmap-method | Heatmap |
| plotCounts | Plot counts |
| plotCounts-method | Plot counts |
| plotCountsPerBiotype | Plot counts per biotype |
| plotCountsPerBiotype-method | Plot counts per biotype |
| plotCountsPerBroadClass-method | Plot counts per biotype |
| plotCountsPerGene | Plot counts per gene |
| plotCountsPerGene-method | Plot counts per gene |
| plotGenderMarkers | Plot sexually dimorphic gender marker genes |
| plotGenderMarkers-method | Plot sexually dimorphic gender marker genes |
| plotGenesDetected | Plot genes detected |
| plotGenesDetected-method | Plot genes detected |
| plotHeatmap | Heatmap |
| plotHeatmap-method | Heatmap |
| plotPCA | Principal component analysis plot |
| plotPCA-method | Principal component analysis plot |
| plotQC | Quality control |
| plotQC-method | Quality control |
| plotQuantileHeatmap-method | Heatmap |
| plotTotalCounts | Plot total read counts |
| plotTotalCounts-method | Plot total read counts |
| plotZerosVsDepth | Plot percentage of zeros vs. library depth |
| plotZerosVsDepth-method | Plot percentage of zeros vs. library depth |
| prepareTemplate | Prepare R Markdown template |
| relevel | Relevel row or column data |
| relevelColData | Relevel row or column data |
| relevelRowRanges | Relevel row or column data |
| removeNA | Remove rows and columns containing only 'NA' values |
| removeNA-method | Remove rows and columns containing only 'NA' values |
| rse | Example 'SummarizedExperiment' |
| sampleData | Sample data |
| sampleData-method | Sample data |
| sampleData<--method | Sample data |
| sampleNames | Sample names |
| sampleNames-method | Sample data |
| sampleNames<- | Sample names |
| sampleNames<--method | Sample names |
| sanitizeNA | Sanitize 'NA' values |
| sanitizeNA-method | Sanitize 'NA' values |
| sanitizePercent | Sanitize percentage |
| sanitizePercent-method | Sanitize percentage |
| sanitizeSampleData | Sanitize sample data |
| sce | Example 'SingleCellExperiment' |
| selectSamples | Select samples |
| selectSamples-method | Select samples |
| separator | Separator bar |
| show | Show an object |
| show-method | Show an object |
| showSlotInfo | Show slot information |
| sortUnique | Sort and make unique |
| sparse | Example 'sparseMatrix' |
| stripTranscriptVersions | Strip transcript versions |
| stripTranscriptVersions-method | Strip transcript versions |
| subsetPerSample | Subset per sample |
| subsetPerSample-method | Subset per sample |
| summary | Object summaries |
| summary-method | Object summaries |
| tbl | Example 'tibble' ('tbl_df') |
| theme_midnight | ggplot2 themes |
| theme_paperwhite | ggplot2 themes |
| 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 |
| tx_se | Example transcript-level 'SummarizedExperiment' |
| uniteInterestingGroups | Unite interesting groups into a single column |
| uniteInterestingGroups-method | Unite interesting groups into a single column |
| zerosVsDepth | Percentage of zeros vs. library depth |
| zerosVsDepth-method | Percentage of zeros vs. library depth |