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

## Documentation for package ‘scater’ version 1.10.0

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

## Help Pages

scater-package | Single-cell analysis toolkit for expression in R
arrange | Arrange columns (cells) of a SingleCellExperiment object
arrange-method | Arrange columns (cells) of 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
bootstraps<- | Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
bootstraps<--method | Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
calcAverage | Calculate average counts, adjusting for size factors or library size
calcIsExprs | Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels.
calculateAverage | Calculate average counts, adjusting for size factors or library size
calculateCPM | Calculate counts per million (CPM)
calculateFPKM | Calculate fragments per kilobase of exon per million reads mapped (FPKM)
calculateQCMetrics | Calculate QC metrics
calculateTPM | Calculate transcripts-per-million (TPM)
centreSizeFactors | Centre size factors at unity
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.
filter | Return 'SingleCellExperiment' with cells matching conditions.
filter-method | Return 'SingleCellExperiment' with cells matching conditions.
findImportantPCs | Plot the explanatory PCs for each variable
fpkm | Additional accessors for the typical elements of a SingleCellExperiment object.
fpkm<- | Additional accessors for the typical elements of a SingleCellExperiment object.
getBMFeatureAnnos | Get feature annotation information from Biomart
getExplanatoryPCs | Estimate the percentage of variance explained for each gene.
getVarianceExplained | Estimate the percentage of variance explained for each gene.
isOutlier | Identify outlier values
librarySizeFactors | Compute library size factors
multiplot | Multiple plot function for ggplot2 plots
mutate | Add new variables to 'colData(object)'.
mutate-method | Add new variables to 'colData(object)'.
nexprs | Count the number of non-zero counts per cell or feature
normalise | Normalise a SingleCellExperiment object using pre-computed size factors
normalise-method | Normalise a SingleCellExperiment object using pre-computed size factors
normalize | Normalise a SingleCellExperiment object using pre-computed size factors
normalize-method | Normalise a SingleCellExperiment object using pre-computed size factors
normalizeCounts | Divide columns of a count matrix by the size factors
normalizeSCE | Normalise a SingleCellExperiment object using pre-computed size factors
norm_exprs | Additional accessors for the typical elements of a SingleCellExperiment object.
norm_exprs<- | Additional accessors for the typical elements of a SingleCellExperiment object.
plotCellData | Plot column metadata
plotColData | Plot column metadata
plotDiffusionMap | Plot specific reduced dimensions
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
plotExprsFreqVsMean | Plot frequency against mean for each feature
plotExprsVsTxLength | Plot expression against transcript length
plotFeatureData | Plot row metadata
plotHeatmap | Plot heatmap of gene expression values
plotHighestExprs | Plot the highest expressing features
plotMDS | Plot specific reduced dimensions
plotPCA | Plot specific reduced dimensions
plotPCA-method | Plot specific reduced dimensions
plotPCASCE | Plot specific reduced dimensions
plotPhenoData | Plot column metadata
plotPlatePosition | Plot cells in plate positions
plotQC | Produce QC diagnostic plots
plotReducedDim | Plot reduced dimensions
plotRLE | Plot a relative log expression (RLE) plot
plotRLE-method | Plot a relative log expression (RLE) plot
plotRowData | Plot row metadata
plotScater | Plot an overview of expression for each cell
plotTSNE | Plot specific reduced dimensions
plotUMAP | Plot specific reduced dimensions
readKallistoResults | Read transcript quantification data
readSalmonResults | Read transcript quantification data
readSparseCounts | Read sparse count matrix from file
readTxResults | Read transcript quantification data
Reduced dimension plots | Plot specific reduced dimensions
rename | Rename variables of 'colData(object)'.
rename-method | Rename variables of 'colData(object)'.
runDiffusionMap | Create a diffusion map from cell-level data
runMDS | Perform MDS on cell-level data
runPCA | Perform PCA on cell-level data
runTSNE | Perform t-SNE on cell-level data
runUMAP | Perform UMAP on cell-level data
scater-plot-args | General visualization parameters
scater-vis-var | Variable selection for visualization
SCESet | The "Single Cell Expression Set" (SCESet) class
SCESet-class | The "Single Cell Expression Set" (SCESet) class
sc_example_cell_info | Cell information for the small example single-cell counts dataset to demonstrate capabilities of scater
sc_example_counts | A small example of single-cell counts dataset to demonstrate capabilities of scater
stand_exprs | Additional accessors for the typical elements of a SingleCellExperiment object.
stand_exprs<- | Additional accessors for the typical elements of a SingleCellExperiment object.
sumCountsAcrossFeatures | Sum counts across a feature set
summariseExprsAcrossFeatures | Summarise expression values across feature
toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object
uniquifyFeatureNames | Make feature names unique
updateSCESet | Convert an SCESet object to a SingleCellExperiment object