Single-Cell Analysis Toolkit for Gene Expression Data in R


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Documentation for package ‘scater’ version 1.14.0

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

-- A --

addPerCellQC Add QC to an SE
addPerFeatureQC Add QC to an SE
aggregateAcrossCells Sum counts across sets of cells
aggregateAcrossCells-method Sum counts across sets 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 --

calcAverage Calculate per-feature average counts
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
calculatePCA Perform PCA on expression data
calculatePCA-method Perform PCA on expression data
calculateQCMetrics Calculate QC metrics
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 Centre size factors at unity
computeLibraryFactors Compute library size factors

-- 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<- 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

-- 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 --

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 Normalize a SingleCellExperiment object using pre-computed size factors
normalize-method Normalize a SingleCellExperiment object using pre-computed size factors
normalizeCounts Compute normalized expression values
normalizeCounts-method Compute normalized expression values
normalizeSCE Normalize 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.
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 Per-cell quality control metrics
perCellQCMetrics-method Per-cell quality control metrics
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
plotExprsFreqVsMean Plot frequency against mean for each feature
plotExprsVsTxLength Plot expression against transcript length
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
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
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-red-dim-args Dimensionality reduction options
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<- Additional accessors for the typical elements of a SingleCellExperiment object.
sumCountsAcrossCells Sum counts across sets of cells
sumCountsAcrossCells-method Sum counts across sets 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