Man pages for acidgenomics/bioverbs
S4 Generics for Acid Genomics R Packages

acidgenerics-packageacidgenerics
aggregateCellsToSamplesAggregate cells to samples
aggregateColsAggregate columns
aggregateReplicatesAggregate technical replicates
aggregateRowsAggregate rows
alphaSummaryAlpha level cutoff summary statistics
alphaThresholdAlpha threshold
as.DataFrameCoerce object to S4 DataFrame
as.SummarizedExperimentCoerce object to SummarizedExperiment
atomizeAtomize
autopadZerosAutopad zeros
barcodeRanksPerSampleBarcode ranks per sample
calculateMetricsCalculate quality control metrics
cell2sampleCell-to-sample mappings
cellCountsPerClusterCell counts per cluster
cellTypesPerClusterCell types per cluster
clustersCluster identifiers
coerceToListCoerce to list
collapseToStringCollapse to string
collectionNamesGene set collection names
contrastNameContrast name
contrastNamesContrast names
contrastSamplesSamples corresponding to a differential expression contrast
convertGenesToSymbolsConvert genes to symbols
convertSampleIDsToNamesConvert sample identifiers to names
convertSymbolsToGenesConvert symbols to genes
convertTranscriptsToGenesConvert transcripts to genes
correlationCorrelation
cpmCounts per million
defunctDefunct functions
degDifferentially expressed genes
deprecatedDeprecated functions
diffExpDifferential expression
diffExpPerClusterDifferential expression per cluster
encodeEncode using run-length encoding
enrichedGeneSetsEnriched gene sets
exportExport
factorizeFactorize
filterCellsFilter cells
findMarkersFind cluster-specific marker genes
foldChangeToLogRatioFold change to log ratio
fpkmFragments per kilobase per million mapped fragments
geneNamesGene names
geometricMeanGeometric mean
headtailReturn the first and last parts of an object
humanizeHumanize an R object
interestingGroupsInteresting groups
joinJoin operations
lfcThresholdLog2 fold change threshold
logRatioToFoldChangeLog ratio to fold change
mapGenesToIDsMap genes (gene names) to gene identifiers
mapGenesToRownamesMap genes to row names
mapGenesToSymbolsMap genes (gene identifiers) to gene names (symbols)
markdownMarkdown
matchRowNameColumnMatch row name column
mcolnamesMetadata column names
meltMelt columns into key-value pairs
metadata2Metadata
metricsQuality control metrics
metricsPerSampleQuality control metrics per sample
mutateMutate multiple columns
nonzeroRowsAndColsSubset object to keep only non-zero rows and columns
plot5Prime3PrimeBiasPlot 5' to 3' bias
plotBarcodeRanksPlot barcode ranks
plotCellCountsPlot cell counts
plotCellCountsPerClusterPlot cell counts per cluster
plotCellsPlot cells
plotCellTypesPerClusterPlot cell types per cluster
plotCorrelationHeatmapCorrelation heatmap
plotCountDensityPlot count density
plotCountsPlot counts
plotCountsCorrelationPlot counts correlation
plotCountsCorrelationHeatmapPlot counts correlation heatmap
plotCountsPerBiotypePlot counts per biotype
plotCountsPerBroadClassPlot counts per broad class definition
plotCountsPerCellPlot counts per cell
plotCountsPerFeaturePlot counts per feature
plotCountsPerGenePlot counts per gene
plotCountsVsFeaturesPlot count and feature correlation
plotDEGHeatmapDifferentially expressed gene heatmap
plotDEGPCAPlot differentially expressed gene principal component...
plotDEGUpsetUpSet plot of directional DEG intersections across contrasts
plotDotsDot plot
plotEnrichedGeneSetsPlot enriched gene sets
plotEnrichedUpsetUpSet plot of directional enriched pathway intersections...
plotExonicMappingRatePlot exonic mapping rate
plotFeaturePlot feature
plotFeaturesDetectedPlot features detected
plotFeaturesPerCellPlot features per cell
plotGenderMarkersPlot sexually dimorphic gender marker genes
plotGeneSaturationPlot gene detection saturation
plotHeatmapHeatmap
plotIntergenicMappingRatePlot intergenic mapping rate
plotIntronicMappingRatePlot intronic mapping rate
plotKnownMarkersPlot known markers
plotMappedReadsPlot mapped reads
plotMappingRatePlot mapping rate
plotMarkerPlot cell-type-specific gene markers
plotMeanSDPlot row standard deviations vs. row means
plotMitoRatioPlot mitochondrial transcript abundance
plotMitoVsCodingPlot mitochondrial vs. coding counts
plotNoveltyPlot novelty score
plotPCACovariatesFind correlation between principal components (PCs) and...
plotPCElbowPlot principal component elbow
plotQCQuality control
plotQuantileHeatmapQuantile heatmap
plotReadsPerCellPlot read counts per cell
plotReducedDimPlot reduced dimensions
plotRRNAMappingRatePlot ribosomal RNA (rRNA) mapping rate
plotSumsPlot row or column sums
plotTopMarkersPlot top markers
plotTotalCountsPlot total read counts
plotTotalReadsPlot total reads
plotTSNEt-SNE plot
plotUMAPUMAP plot
plotUpsetUpSet plot
plotViolinViolin plot
plotVolcanoVolcano plot
plotZerosVsDepthPlot percentage of zeros vs. library depth
pseudobulkPseudobulk
rankedListRanked list
relativeLogExpressionRelative log expression
removeNARemove rows and columns containing only NA values
resultsResults
resultsMatrixResults matrix
resultsNamesResults names
resultsTablesResults tables
sampleDataSample data
sanitizeNASanitize NA values
sanitizePercentSanitize percentage
selectSelect multiple columns
selectSamplesSelect samples
stripTranscriptVersionsStrip transcript versions
subsetPerSampleSubset per sample
tmmTrimmed mean of M-values
topCellsPerSampleTop cells per sample
topMarkersTop markers
topTablesTop tables
tpmTranscripts per million
uniteInterestingGroupsUnite interesting groups into a single column
zerosVsDepthPercentage of zeros vs. library depth
acidgenomics/bioverbs documentation built on Jan. 19, 2020, 8:18 a.m.