Single-Cell Analysis Toolkit for Gene Expression Data in R


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Documentation for package ‘scater’ version 1.10.1

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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