Single-Cell Analysis Toolkit for Gene Expression Data in R

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Documentation for package ‘scater’ version 1.26.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotateBMFeatures	Get feature annotation information from Biomart
bootstraps	Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
bootstraps-method	Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
bootstraps<-	Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
bootstraps<--method	Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
calculateDiffusionMap	Defunct functions
calculateDiffusionMap-method	Defunct functions
calculateMDS	Perform MDS on cell-level data
calculateMDS-method	Perform MDS on cell-level data
calculateMultiUMAP	Multi-modal UMAP
calculateMultiUMAP-method	Multi-modal UMAP
calculateNMF	Perform NMF on cell-level data
calculateNMF-method	Perform NMF on cell-level data
calculatePCA	Perform PCA on expression data
calculatePCA-method	Perform PCA on expression data
calculateQCMetrics	Defunct functions
calculateTSNE	Perform t-SNE on cell-level data
calculateTSNE-method	Perform t-SNE on cell-level data
calculateUMAP	Perform UMAP on cell-level data
calculateUMAP-method	Perform UMAP on cell-level data
centreSizeFactors	Defunct functions
defunct	Defunct functions
exprs	Additional accessors for the typical elements of a SingleCellExperiment object.
exprs,SingleCellExperiment-method,	Additional accessors for the typical elements of a SingleCellExperiment object.
exprs<--method	Additional accessors for the typical elements of a SingleCellExperiment object.
fpkm	Additional accessors for the typical elements of a SingleCellExperiment object.
fpkm-method	Additional accessors for the typical elements of a SingleCellExperiment object.
fpkm<-	Additional accessors for the typical elements of a SingleCellExperiment object.
fpkm<--method	Additional accessors for the typical elements of a SingleCellExperiment object.
getBMFeatureAnnos	Get feature annotation information from Biomart
getExplanatoryPCs	Per-PC variance explained by a variable
getVarianceExplained	Per-gene variance explained by a variable
getVarianceExplained-method	Per-gene variance explained by a variable
ggcells	Create a ggplot from a SingleCellExperiment
ggfeatures	Create a ggplot from a SingleCellExperiment
multiplot	Multiple plot function for ggplot2 plots
nexprs	Count the number of non-zero counts per cell or feature
nexprs-method	Count the number of non-zero counts per cell or feature
normalize-method	Defunct functions
norm_exprs	Additional accessors for the typical elements of a SingleCellExperiment object.
norm_exprs-method	Additional accessors for the typical elements of a SingleCellExperiment object.
norm_exprs<-	Additional accessors for the typical elements of a SingleCellExperiment object.
norm_exprs<--method	Additional accessors for the typical elements of a SingleCellExperiment object.
plotColData	Plot column metadata
plotDiffusionMap	Plot specific reduced dimensions
plotDots	Create a dot plot of expression values
plotExplanatoryPCs	Plot the explanatory PCs for each variable
plotExplanatoryVariables	Plot explanatory variables ordered by percentage of variance explained
plotExpression	Plot expression values for all cells
plotGroupedHeatmap	Plot heatmap of group-level expression averages
plotHeatmap	Plot heatmap of gene expression values
plotHighestExprs	Plot the highest expressing features
plotMDS	Plot specific reduced dimensions
plotNMF	Plot specific reduced dimensions
plotPCA	Plot specific reduced dimensions
plotPCA-method	Plot specific reduced dimensions
plotPCASCE	Plot specific reduced dimensions
plotPlatePosition	Plot cells in plate positions
plotReducedDim	Plot reduced dimensions
plotRLE	Plot relative log expression
plotRLE-method	Plot relative log expression
plotRowData	Plot row metadata
plotScater	Plot an overview of expression for each cell
plotTSNE	Plot specific reduced dimensions
plotUMAP	Plot specific reduced dimensions
projectReducedDim	Project cells into an arbitrary dimensionality reduction space.
projectReducedDim-method	Project cells into an arbitrary dimensionality reduction space.
Reduced dimension plots	Plot specific reduced dimensions
retrieveCellInfo	Cell-based data retrieval
retrieveFeatureInfo	Feature-based data retrieval
runColDataPCA	Perform PCA on column metadata
runDiffusionMap	Defunct functions
runMDS	Perform MDS on cell-level data
runMultiUMAP	Multi-modal UMAP
runNMF	Perform NMF on cell-level data
runPCA	Perform PCA on expression data
runPCA-method	Perform PCA on expression data
runTSNE	Perform t-SNE on cell-level data
runUMAP	Perform UMAP on cell-level data
scater-pkg	The 'scater' package
scater-plot-args	General visualization parameters
SCESet	The "Single Cell Expression Set" (SCESet) class
SCESet-class	The "Single Cell Expression Set" (SCESet) class
stand_exprs	Additional accessors for the typical elements of a SingleCellExperiment object.
stand_exprs,SingleCellExperiment-method,	Additional accessors for the typical elements of a SingleCellExperiment object.
stand_exprs<-	Additional accessors for the typical elements of a SingleCellExperiment object.
stand_exprs<--method	Additional accessors for the typical elements of a SingleCellExperiment object.
toSingleCellExperiment	Convert an SCESet object to a SingleCellExperiment object
updateSCESet	Convert an SCESet object to a SingleCellExperiment object