Man pages for davismcc/scater
Single-Cell Analysis Toolkit for Gene Expression Data in R

accessorsAdditional accessors for the typical elements of a...
arrangeArrange columns (cells) of a SingleCellExperiment object
bootstrapsAccessor and replacement for bootstrap results in a...
calculateAverageCalculate average counts, adjusting for size factors or...
calculateCPMCalculate counts per million (CPM)
calculateFPKMCalculate fragments per kilobase of exon per million reads...
calculateQCMetricsCalculate QC metrics
calculateTPMCalculate transcripts-per-million (TPM)
centreSizeFactorsCentre size factors at unity
filterReturn 'SingleCellExperiment' with cells matching conditions.
getBMFeatureAnnosGet feature annotation information from Biomart
getExplanatoryPCsEstimate the percentage of variance explained for each gene.
getVarianceExplainedEstimate the percentage of variance explained for each gene.
isOutlierIdentify outlier values
librarySizeFactorsCompute library size factors
multiplotMultiple plot function for ggplot2 plots
mutateAdd new variables to 'colData(object)'.
nexprsCount the number of non-zero counts per cell or feature
normalizeNormalize a SingleCellExperiment object using pre-computed...
normalizeCountsDivide columns of a count matrix by the size factors
plotColDataPlot column metadata
plotExplanatoryPCsPlot the explanatory PCs for each variable
plotExplanatoryVariablesPlot explanatory variables ordered by percentage of variance...
plotExpressionPlot expression values for all cells
plotExprsFreqVsMeanPlot frequency against mean for each feature
plotExprsVsTxLengthPlot expression against transcript length
plotHeatmapPlot heatmap of gene expression values
plotHighestExprsPlot the highest expressing features
plotPlatePositionPlot cells in plate positions
plot_reddimPlot specific reduced dimensions
plotReducedDimPlot reduced dimensions
plotRLEPlot a relative log expression (RLE) plot
plotRowDataPlot row metadata
plotScaterPlot an overview of expression for each cell
readSparseCountsRead sparse count matrix from file
renameRename variables of 'colData(object)'.
runDiffusionMapCreate a diffusion map from cell-level data
runMDSPerform MDS on cell-level data
runPCAPerform PCA on cell-level data
runTSNEPerform t-SNE on cell-level data
runUMAPPerform UMAP on cell-level data
scater-packageSingle-cell analysis toolkit for expression in R
scater-plot-argsGeneral visualization parameters
scater-vis-varVariable selection for visualization
SCESetThe "Single Cell Expression Set" (SCESet) class
sc_example_cell_infoCell information for the small example single-cell counts...
sc_example_countsA small example of single-cell counts dataset to demonstrate...
sumCountsAcrossFeaturesSum counts across a feature set
toSingleCellExperimentConvert an SCESet object to a SingleCellExperiment object
uniquifyFeatureNamesMake feature names unique
davismcc/scater documentation built on Nov. 29, 2018, 5:27 a.m.