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

accessorsAdditional accessors for the typical elements of a...
annotateBMFeaturesGet feature annotation information from Biomart
batchCorrectedAveragesCompute batch-corrected group-level averages
bootstrapsAccessor and replacement for bootstrap results in a...
defunctDefunct functions
getExplanatoryPCsPer-PC variance explained by a variable
getVarianceExplainedPer-gene variance explained by a variable
ggsceCreate a ggplot from a SingleCellExperiment
multiplotMultiple plot function for ggplot2 plots
nexprsCount the number of non-zero counts per cell or feature
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
plotGroupedHeatmapPlot heatmap of group-level expression averages
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
reexportsObjects exported from other packages
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-pkgThe 'scater' package
scater-plot-argsGeneral visualization parameters
SCESetThe "Single Cell Expression Set" (SCESet) class
toSingleCellExperimentConvert an SCESet object to a SingleCellExperiment object
scater documentation built on Feb. 28, 2021, 2:01 a.m.