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

## Documentation for package ‘scater’ version 1.16.1

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

## Help Pages

A B C D E F G I L M N P Q R S T U misc

## -- A --

addPerCellQC | Add QC to an SE
addPerFeatureQC | Add QC to an SE
aggregateAcrossCells | Aggregate expression values across groups of cells
aggregateAcrossCells-method | Aggregate expression values across groups of cells
aggregateAcrossFeatures | Sum counts across feature sets
annotateBMFeatures | Get feature annotation information from Biomart

## -- B --

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

## -- C --

calculateAverage | Calculate per-feature average counts
calculateAverage-method | Calculate per-feature average counts
calculateCPM | Calculate counts per million (CPM)
calculateCPM-method | Calculate counts per million (CPM)
calculateDiffusionMap | Create a diffusion map from cell-level data
calculateDiffusionMap-method | Create a diffusion map from cell-level data
calculateFPKM | Calculate FPKMs
calculateMDS | Perform MDS on cell-level data
calculateMDS-method | Perform MDS on cell-level data
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
calculateTPM | Calculate TPMs
calculateTPM-method | Calculate TPMs
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
computeLibraryFactors | Compute library size factors
computeMedianFactors | Compute median-based size factors

## -- D --

defunct | Defunct functions

## -- E --

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.

## -- F --

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.

## -- G --

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

## -- I --

isOutlier | Identify outlier values

## -- L --

librarySizeFactors | Compute library size factors
librarySizeFactors-method | Compute library size factors
logNormCounts | Compute log-normalized expression values
logNormCounts-method | Compute log-normalized expression values

## -- M --

makePerCellDF | Create a per-cell data.frame from a SingleCellDataFrame
makePerFeatureDF | Create a per-feature data.frame from a SingleCellDataFrame
medianSizeFactors | Compute median-based size factors
medianSizeFactors-method | Compute median-based size factors
mockSCE | Mock up a SingleCellExperiment
multiplot | Multiple plot function for ggplot2 plots

## -- N --

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
normalizeCounts | Compute normalized expression values
normalizeCounts-method | Compute normalized expression values
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.
numDetectedAcrossCells | Number of detected expression values per group of cells
numDetectedAcrossCells-method | Number of detected expression values per group of cells
numDetectedAcrossFeatures | Number of detected expression values per group of features
numDetectedAcrossFeatures-method | Number of detected expression values per group of features

## -- P --

perCellQCMetrics | Compute per-cell quality control metrics for a count matrix or a SingleCellExperiment.
perCellQCMetrics-method | Compute per-cell quality control metrics for a count matrix or a SingleCellExperiment.
perFeatureQCMetrics | Per-feature quality control metrics
perFeatureQCMetrics-method | Per-feature quality control metrics
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
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

## -- Q --

quickPerCellQC | Quick cell-level QC

## -- R --

readSparseCounts | Read sparse count matrix from file
Reduced dimension plots | Plot specific reduced dimensions
retrieveCellInfo | Cell-based data retrieval
retrieveFeatureInfo | Feature-based data retrieval
runColDataPCA | Perform PCA on column metadata
runDiffusionMap | Create a diffusion map from cell-level data
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

## -- S --

scater-plot-args | General visualization parameters
scater-utils | Developer utilities
SCESet | The "Single Cell Expression Set" (SCESet) class
SCESet-class | The "Single Cell Expression Set" (SCESet) class
sc_example_cell_info | Mock up a SingleCellExperiment
sc_example_counts | Mock up a SingleCellExperiment
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.
sumCountsAcrossCells | Aggregate expression values across groups of cells
sumCountsAcrossCells-method | Aggregate expression values across groups of cells
sumCountsAcrossFeatures | Sum counts across feature sets
sumCountsAcrossFeatures-method | Sum counts across feature sets

## -- T --

toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object

## -- U --

uniquifyFeatureNames | Make feature names unique
updateSCESet | Convert an SCESet object to a SingleCellExperiment object

## -- misc --

.assignIndicesToWorkers | Developer utilities
.bpNotSharedOrUp | Developer utilities
.splitColsByWorkers | Developer utilities
.splitRowsByWorkers | Developer utilities
.splitVectorByWorkers | Developer utilities
.subset2index | Developer utilities