# Single-cell analysis toolkit for gene expression data in R

## Documentation for package ‘scater’ version 1.6.0

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

## Help Pages

A B C D E F G I K M N P R S T U

scater-package | Single-cell analysis toolkit for expression in R

## -- A --

accessors | Additional accessors for the typical elements of a SingleCellExperiment object.
areSizeFactorsCentred | Check if the size factors are centred at unity
arrange | Arrange columns (cells) of a SingleCellExperiment object
arrange-method | Arrange columns (cells) of a SingleCellExperiment object

## -- 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 --

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.
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)

## -- D --

deprecated | Retrieve a representation of gene expression
downsampleCounts | Downsample a count matrix

## -- 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 --

filter | Return 'SingleCellExperiment' with cells matching conditions.
filter-method | Return 'SingleCellExperiment' with cells matching conditions.
findImportantPCs | Find most important principal components for a given variable
fpkm | Additional accessors for the typical elements of a SingleCellExperiment object.
fpkm<- | Additional accessors for the typical elements of a SingleCellExperiment object.
fromCellDataSet | Retrieve a representation of gene expression

## -- G --

getBMFeatureAnnos | Get feature annotation information from Biomart
getExprs | Retrieve a representation of gene expression

## -- I --

isOutlier | Identify if a cell is an outlier based on a metric

## -- K --

kallisto-wrapper | kallisto wrapper functions

## -- M --

multiplot | Multiple plot function for ggplot2 plots
mutate | Add new variables to 'colData(object)'.
mutate-method | Add new variables to 'colData(object)'.

## -- N --

newSCESet | Create a new SCESet object
nexprs | Count the number of expressed genes per cell
normalise | Normalise a SingleCellExperiment object using pre-computed size factors
normalise-method | Normalise a SingleCellExperiment object using pre-computed size factors
normaliseExprs | Normalise expression expression levels for an SingleCellExperiment object
normalize | Normalise a SingleCellExperiment object using pre-computed size factors
normalize-method | Normalise a SingleCellExperiment object using pre-computed size factors
normalizeExprs | Normalise expression expression levels for an SingleCellExperiment object
normalizeSCE | Normalise a SingleCellExperiment object using pre-computed size factors
normliseExprs | Normalise expression expression levels for an SingleCellExperiment object
norm_exprs | Additional accessors for the typical elements of a SingleCellExperiment object.
norm_exprs<- | Additional accessors for the typical elements of a SingleCellExperiment object.

## -- P --

plotCellData | Plot cell phenotype data from an SingleCellExperiment object
plotColData | Plot cell phenotype data from an SingleCellExperiment object
plotDiffusionMap | Plot a diffusion map for a SingleCellExperiment object
plotDiffusionMap-method | Plot a diffusion map for a SingleCellExperiment object
plotExplanatoryVariables | Plot explanatory variables ordered by percentage of phenotypic variance explained
plotExpression | Plot expression values for a set of features (e.g. genes or transcripts)
plotExpression-method | Plot expression values for a set of features (e.g. genes or transcripts)
plotExpressionDefault | Plot expression values for a set of features (e.g. genes or transcripts)
plotExprsFreqVsMean | Plot frequency of expression against mean expression level
plotExprsVsTxLength | Plot expression against transcript length
plotFeatureData | Plot feature (gene) data from a SingleCellExperiment object
plotHighestExprs | Plot the features with the highest expression values
plotMDS | Produce a multidimensional scaling plot for a SingleCellExperiment object
plotMDS-method | Produce a multidimensional scaling plot for a SingleCellExperiment object
plotMetadata | Plot metadata for cells or features
plotPCA | Plot PCA for a SingleCellExperiment object
plotPCA-method | Plot PCA for a SingleCellExperiment object
plotPCASCE | Plot PCA for a SingleCellExperiment object
plotPhenoData | Plot cell phenotype data from an SingleCellExperiment object
plotPlatePosition | Plot cells in plate positions
plotQC | Produce QC diagnostic plots
plotReducedDim | Plot reduced dimension representation of cells
plotReducedDim-method | Plot reduced dimension representation of cells
plotReducedDimDefault | Plot reduced dimension representation of cells
plotRLE | Plot a relative log expression (RLE) plot
plotRLE-method | Plot a relative log expression (RLE) plot
plotRowData | Plot feature (gene) data from a SingleCellExperiment object
plotScater | Plot an overview of expression for each cell
plotTSNE | Plot t-SNE for an SingleCellExperiment object
plotTSNE-method | Plot t-SNE for an SingleCellExperiment object

## -- R --

read10XResults | Load in data from 10x experiment
read10xResults | Load in data from 10x experiment
readKallistoResults | kallisto wrapper functions
readKallistoResultsOneSample | kallisto wrapper functions
readSalmonResults | Salmon wrapper functions
readSalmonResultsOneSample | Salmon wrapper functions
readTxResults | Read transcript quantification data with tximport package
rename | Rename variables of 'colData(object)'.
rename-method | Rename variables of 'colData(object)'.
runDiffusionMap | Plot a diffusion map for a SingleCellExperiment object
runKallisto | kallisto wrapper functions
runPCA | Plot PCA for a SingleCellExperiment object
runSalmon | Salmon wrapper functions
runTSNE | Plot t-SNE for an SingleCellExperiment object

## -- S --

salmon-wrapper | Salmon wrapper functions
scater_gui | scater GUI function
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.
summariseExprsAcrossFeatures | Summarise expression values across feature

## -- T --

toCellDataSet | Retrieve a representation of gene expression
toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object

## -- U --

updateSCESet | Convert an SCESet object to a SingleCellExperiment object