Man pages for scater
Single-Cell Analysis Toolkit for Gene Expression Data in R

accessorsAdditional accessors for the typical elements of a...
addPerCellQCAdd QC to an SE
annotateBMFeaturesGet feature annotation information from Biomart
bootstrapsAccessor and replacement for bootstrap results in a...
calculateAverageCalculate per-feature average counts
calculateCPMCalculate counts per million (CPM)
calculateFPKMCalculate FPKMs
calculateTPMCalculate TPMs
defunctDefunct functions
getExplanatoryPCsPer-PC variance explained by a variable
getVarianceExplainedPer-gene variance explained by a variable
ggsceCreate a ggplot from a SingleCellExperiment
isOutlierIdentify outlier values
librarySizeFactorsCompute library size factors
logNormCountsCompute log-normalized expression values
makePerCellDFCreate a per-cell data.frame from a SingleCellDataFrame
makePerFeatureDFCreate a per-feature data.frame from a SingleCellDataFrame
medianSizeFactorsCompute median-based size factors
mockSCEMock up a SingleCellExperiment
multiplotMultiple plot function for ggplot2 plots
nexprsCount the number of non-zero counts per cell or feature
normalizeCountsCompute normalized expression values
numDetectedAcrossCellsNumber of detected expression values per group of cells
numDetectedAcrossFeaturesNumber of detected expression values per group of features
perCellQCMetricsCompute per-cell quality control metrics for a count matrix...
perFeatureQCMetricsPer-feature quality control metrics
plotColDataPlot column metadata
plotDotsCreate a dot plot of expression values
plotExplanatoryPCsPlot the explanatory PCs for each variable
plotExplanatoryVariablesPlot explanatory variables ordered by percentage of variance...
plotExpressionPlot expression values for all cells
plotHeatmapPlot heatmap of gene expression values
plotHighestExprsPlot the highest expressing features
plotPlatePositionPlot cells in plate positions
plot_reddimPlot specific reduced dimensions
plotReducedDimPlot reduced dimensions
plotRLEPlot relative log expression
plotRowDataPlot row metadata
plotScaterPlot an overview of expression for each cell
quickPerCellQCQuick cell-level QC
readSparseCountsRead sparse count matrix from file
retrieveCellInfoCell-based data retrieval
retrieveFeatureInfoFeature-based data retrieval
runColDataPCAPerform PCA on column metadata
runDiffusionMapCreate a diffusion map from cell-level data
runMDSPerform MDS on cell-level data
runMultiUMAPMulti-modal UMAP
runNMFPerform NMF on cell-level data
runPCAPerform PCA on expression data
runTSNEPerform t-SNE on cell-level data
runUMAPPerform UMAP on cell-level data
scater-plot-argsGeneral visualization parameters
scater-utilsDeveloper utilities
SCESetThe "Single Cell Expression Set" (SCESet) class
sumCountsAcrossCellsAggregate expression values across groups of cells
sumCountsAcrossFeaturesSum counts across feature sets
toSingleCellExperimentConvert an SCESet object to a SingleCellExperiment object
uniquifyFeatureNamesMake feature names unique
scater documentation built on June 28, 2020, 2 a.m.