# Single-Cell Analysis Toolkit for Gene Expression Data in R

## Documentation for package ‘scater’ version 1.39.0

- 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 | Defunct functions
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