scater
Single-Cell Analysis Toolkit for Gene Expression Data in R

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Functions
203
Source code
57
Man pages
39
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scater: Single-Cell Analysis Toolkit for Gene Expression Data in R
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API

API for scater
Single-Cell Analysis Toolkit for Gene Expression Data in R

Global functions
.add_extra_guide Source code
.add_other_or_warn Source code
.aes_in_use Source code
.calculate_diffusion_map Source code
.calculate_mds Source code
.calculate_nmf Source code
.calculate_pca Source code
.calculate_tsne Source code
.calculate_umap Source code
.central_plotter Source code
.choose_nthreads Source code
.coerce_to_factor Source code
.compute_multi_modal_metrics Source code
.get_mat_for_reddim Source code
.get_mat_from_sce Source code
.get_palette Source code
.get_point_args Source code
.get_rowData_column Source code
.get_variance_explained Source code
.incorporate_common_vis_col Source code
.incorporate_common_vis_row Source code
.makePairs Source code
.nexprs Source code
.plotRLE_full Source code
.plotRLE_minimal Source code
.resolve_plot_colours Source code
.rle_boxplot_stats Source code
.swap_rownames Source code
GET_FUN Source code
Reduced dimension plots Man page
SCESet Man page
SCESet-class Man page
SET_FUN Source code
addPerCellQC Man page
addPerFeatureQC Man page
aggregateAcrossCells Man page
aggregateAcrossFeatures Man page
annotateBMFeatures Man page Source code
batchCorrectedAverages Man page Source code
bootstraps Man page
bootstraps,SingleCellExperiment-method Man page
bootstraps<- Man page
bootstraps<-,SingleCellExperiment,array-method Man page
calculateAverage Man page
calculateCPM Man page
calculateDiffusionMap Man page
calculateDiffusionMap,ANY-method Man page
calculateDiffusionMap,SingleCellExperiment-method Man page
calculateDiffusionMap,SummarizedExperiment-method Man page
calculateFPKM Man page
calculateMDS Man page
calculateMDS,ANY-method Man page
calculateMDS,SingleCellExperiment-method Man page
calculateMDS,SummarizedExperiment-method Man page
calculateMultiUMAP Man page
calculateMultiUMAP,ANY-method Man page
calculateMultiUMAP,SingleCellExperiment-method Man page
calculateMultiUMAP,SummarizedExperiment-method Man page
calculateNMF Man page
calculateNMF,ANY-method Man page
calculateNMF,SingleCellExperiment-method Man page
calculateNMF,SummarizedExperiment-method Man page
calculatePCA Man page
calculatePCA,ANY-method Man page
calculatePCA,SingleCellExperiment-method Man page
calculatePCA,SummarizedExperiment-method Man page
calculateQCMetrics Man page Source code
calculateTPM Man page
calculateTSNE Man page
calculateTSNE,ANY-method Man page
calculateTSNE,SingleCellExperiment-method Man page
calculateTSNE,SummarizedExperiment-method Man page
calculateUMAP Man page
calculateUMAP,ANY-method Man page
calculateUMAP,SingleCellExperiment-method Man page
calculateUMAP,SummarizedExperiment-method Man page
centreSizeFactors Man page Source code
computeLibraryFactors Man page
computeMedianFactors Man page
defunct Man page
exprs Man page
exprs,SingleCellExperiment-method, Man page
exprs<-,SingleCellExperiment,ANY-method Man page
fpkm Man page
fpkm,SingleCellExperiment-method Man page
fpkm<- Man page
fpkm<-,SingleCellExperiment,ANY-method Man page
getBMFeatureAnnos Man page Source code
getExplanatoryPCs Man page Source code
getVarianceExplained Man page
getVarianceExplained,ANY-method Man page
getVarianceExplained,SummarizedExperiment-method Man page
ggcells Man page Source code
ggfeatures Man page Source code
isOutlier Man page
librarySizeFactors Man page
logNormCounts Man page
makePerCellDF Man page
makePerFeatureDF Man page
medianSizeFactors Man page
mockSCE Man page
multiplot Man page Source code
nexprs Man page
nexprs,ANY-method Man page
nexprs,SummarizedExperiment-method Man page
norm_exprs Man page
norm_exprs,SingleCellExperiment-method Man page
norm_exprs<- Man page
norm_exprs<-,SingleCellExperiment,ANY-method Man page
normalize,SingleCellExperiment-method Man page
normalizeCounts Man page
numDetectedAcrossCells Man page
numDetectedAcrossFeatures Man page
paired_reddim_plot Source code
perCellQCMetrics Man page
perFeatureQCMetrics Man page
plotColData Man page Source code
plotDiffusionMap Man page Source code
plotDots Man page Source code
plotExplanatoryPCs Man page Source code
plotExplanatoryVariables Man page Source code
plotExpression Man page Source code
plotGroupedHeatmap Man page Source code
plotHeatmap Man page Source code
plotHighestExprs Man page Source code
plotMDS Man page Source code
plotNMF Man page Source code
plotPCA Man page
plotPCA,SingleCellExperiment-method Man page
plotPCASCE Man page Source code
plotPlatePosition Man page Source code
plotRLE Man page Source code
plotRLE,SingleCellExperiment-method Man page
plotReducedDim Man page Source code
plotRowData Man page Source code
plotScater Man page Source code
plotTSNE Man page Source code
plotUMAP Man page Source code
quickPerCellQC Man page
readSparseCounts Man page
reexports Man page
retrieveCellInfo Man page Source code
retrieveFeatureInfo Man page Source code
runColDataPCA Man page Source code
runDiffusionMap Man page Source code
runMDS Man page Source code
runMultiUMAP Man page Source code
runNMF Man page Source code
runPCA Man page
runPCA,SingleCellExperiment-method Man page
runTSNE Man page Source code
runUMAP Man page Source code
scater-pkg Man page
scater-plot-args Man page
stand_exprs Man page
stand_exprs,SingleCellExperiment-method, Man page
stand_exprs<- Man page
stand_exprs<-,SingleCellExperiment,ANY-method Man page
sumCountsAcrossCells Man page
sumCountsAcrossFeatures Man page
toSingleCellExperiment Man page Source code
top_cumprop Source code
uniquifyFeatureNames Man page
updateSCESet Man page Source code
scater documentation built on Feb. 28, 2021, 2:01 a.m.

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