Man pages for acidgenomics/AcidGenerics
Acid Genomics Generics

aggregateCellsToSamplesAggregate cells to samples
aggregateColsAggregate columns
aggregateRowsAggregate rows
alphaSummaryAlpha level cutoff summary statistics
alphaThresholdAlpha threshold
as.DataFrameCoerce object to S4 DataFrame
as.DESeqDataSetCoerce object to 'DESeqDataSet'
as.DESeqTransformCoerce object to 'DESeqTransform'
as.DGEListCoerce object to 'DGEList'
as.SeuratCoerce object to Seurat
as.SingleCellExperimentCoerce object to 'SingleCellExperiment'
as.SummarizedExperimentCoerce object to SummarizedExperiment
autopadZerosAutopad zeros
barcodeRanksPerSampleBarcode ranks per sample
baseMeanThresholdBase mean threshold
calculateMetricsCalculate quality control metrics
camelCaseCamel case
castCast data from long to wide format
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
convertToHumanConvert data set by mapping to human orthologs
convertTranscriptsToGenesConvert transcripts to genes
cpmCounts per million
degDifferentially expressed genes
degIntersectionIntersection of differentially expressed genes
degPerContrastDifferentially expressed genes per contrast
diffExpDifferential expression
diffExpPerClusterDifferential expression per cluster
dottedCaseDotted case
droplevels2Drop factor levels
encodeEncode using run-length encoding
enrichedGeneSetsEnriched gene sets
Ensembl2EntrezEnsembl-to-Entrez gene identifier mappings
Entrez2EnsemblEntrez-to-Ensembl gene identifier mappings
euclideanCalculate Euclidean distance
filterCellsFilter cells
findMarkersFind cluster-specific marker genes
foldChangeToLogRatioFold change to log ratio
fpkmFragments per kilobase per million mapped fragments
Gene2SymbolGene-to-symbol mappings
geneIDsGene identifiers
geneNamesGene names
geneSetGene set
geneSetNamesGene set names
geneSetResultsGene set results
geometricMeanGeometric mean
headtailReturn the first and last parts of an object
humanizeHumanize an R object
integerCountsInteger counts
interestingGroupsInteresting groups
intersectAllIntersection of more than two vectors
intersectionMatrixIntersection matrix
joinJoin operations
kebabCaseKebab case
KnownMarkersKnown cell markers
leadingEdgeLeading edge genes
lfcShrinkShrink log2 fold changes
lfcShrinkTypeShrunken log2 fold change (LFC) type
lfcThresholdLog2 fold change threshold
logRatioToFoldChangeLog ratio to fold change
makeDimnamesMake syntactically valid dimnames
makeLabelMake a plot axis or legend label out of a character string
makeNamesMake syntactically valid names
makeSampleDataMake sample data
makeTitleMake a title out of character string
makeWordsConvert syntactic names to words separated by spaces
mapCellsMap input to cell identifiers
mapColnamesMap input to column names
mapGenesMap input to gene identifiers
mapGenesToIDsMap genes (gene names) to gene identifiers
mapGenesToRownamesMap genes to row names
mapGenesToSymbolsMap genes (gene identifiers) to gene names (symbols)
mapRownamesMap input to row names
markdownPlotsMarkdown plots
markdownTablesMarkdown tables
matchCellColumnMatch cell identifier column
matchGeneColumnMatch gene identifier column
matchRownameColumnMatch row name column
matchSampleColumnMatch sample identifier column
matchTranscriptColumnMatch transcript identifier column
meltMelt data from wide to long format
metricsQuality control metrics
metricsPerSampleQuality control metrics per sample
mutateMutate multiple columns
nesThresholdNormalized enrichment score (NES) threshold
nonzeroRowsAndColsSubset object to keep only non-zero rows and columns
plot5Prime3PrimeBiasPlot 5' to 3' bias
plotBarcodeRanksPlot barcode ranks
plotBaseMeanPlot base mean distribution
plotCellCountsPlot cell counts
plotCellCountsPerClusterPlot cell counts per cluster
plotCellsPlot cells
plotCellTypesPerClusterPlot cell types per cluster
plotContrastScatterPlot scatterplot of differential expression contrast
plotCorrelationCorrelation X-Y scatterplot
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...
plotDEGStackedBarStacked bar plot of DEGs
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
plotGeneSetPlot gene set enrichment
plotIntergenicMappingRatePlot intergenic mapping rate
plotIntronicMappingRatePlot intronic mapping rate
plotKnownMarkersPlot known markers
plotLFCPlot log2 fold change distributions
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
plotNESPlot normalized enrichment score
plotNoveltyPlot novelty score
plotPCACovariatesFind correlation between principal components (PCs) and...
plotPCElbowPlot principal component elbow
plotPseudoVsAlignedCountsPlot pseudo vs. aligned counts
plotQCQuality control
plotQuantileHeatmapQuantile heatmap
plotReadsPerCellPlot read counts per cell
plotReducedDimPlot reduced dimensions
plotRRNAMappingRatePlot ribosomal RNA (rRNA) mapping rate
plotStackedBarPlotPlot stacked bar plot
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
plotWaterfallPlot waterfall
plotZerosVsDepthPlot percentage of zeros vs. library depth
rankedMatrixCalculate a ranked matrix
rbindToDataFrameRow bind elements 1:1 to a data frame
relativeLogExpressionRelative log expression
removeNARemove rows and columns containing only NA values
resultsDiffRelative difference of results
resultsMatrixResults matrix
resultsNamesResults names
resultsTablesResults tables
sampleDataSample data
sanitizeNASanitize NA values
sanitizePercentSanitize percentage
selectSelect multiple columns
selectSamplesSelect samples
semStandard error of the mean
sentenceCaseSentence case
showHeaderHeader for object show method
slotAlignedCountsSlot aligned counts
snakeCaseSnake case
splitByLevelSplit by factor level
standardizeCellsStandardize cell line names
stripGeneVersionsStrip gene identifier versions
stripTranscriptVersionsStrip transcript identifier versions
subsetPerSampleSubset per sample
tmmTrimmed mean of M-values
topCellsPerSampleTop cells per sample
topMarkersTop markers
tpmTranscripts per million
transcriptIDsTranscript identifiers
transcriptNamesTranscript names
transformTypeVariance-stabilizing transformation type
Tx2GeneTranscript-to-gene mappings
uniteInterestingGroupsUnite interesting groups into a single column
upperCamelCaseUpper camel case
zerosVsDepthPercentage of zeros vs. library depth
zscoreCalculate Z-score
acidgenomics/AcidGenerics documentation built on Feb. 15, 2023, 5:15 p.m.