Single-Cell Analysis Toolkit for Gene Expression Data in R

Documentation for package ‘scater’ version 1.16.2

Help Pages

-- 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 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 --

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 --

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 --

Convert an SCESet object to a SingleCellExperiment object

-- U --

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

-- misc --