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
.assignIndicesToWorkers Man page Source code
.bpNotSharedOrUp Man page Source code
.calculate_average Source code
.calculate_cpm Source code
.calculate_diffusion_map Source code
.calculate_mds Source code
.calculate_nmf Source code
.calculate_pca Source code
.calculate_tpm Source code
.calculate_tsne Source code
.calculate_umap Source code
.center_size_factors Source code
.central_plotter Source code
.choose_assay_names Source code
.coerce_to_factor Source code
.compute_multi_modal_metrics Source code
.create_coldata Source code
.determine_sharingness Source code
.df_to_factor Source code
.downsample_counts Source code
.flatten_nested_dims Source code
.get_altexps_to_use Source code
.get_default_sizes Source code
.get_mat_for_reddim Source code
.get_mat_from_sce Source code
.get_palette Source code
.get_point_args Source code
.get_variance_explained Source code
.harvest_se_by_column Source code
.has_multi_ids Source code
.incorporate_common_vis_col Source code
.incorporate_common_vis_row Source code
.library_size_factors Source code
.makePairs Source code
.median_size_factors Source code
.merge_DF_rows Source code
.nexprs Source code
.nexprs_across_cells Source code
.nexprs_across_features Source code
.noOpSubset Source code
.per_cell_qc_metrics Source code
.per_feature_qc_metrics Source code
.plotRLE_full Source code
.plotRLE_minimal Source code
.process_ids Source code
.resolve_plot_colours Source code
.rle_boxplot_stats Source code
.se_lnc Source code
.splitColsByWorkers Man page Source code
.splitRowsByWorkers Man page Source code
.splitVectorByWorkers Man page Source code
.subset2index Man page Source code
.sum_across_cells Source code
.sum_across_features Source code
.sum_counts_across_cells Source code
.sum_counts_across_features Source code
.transform_sparse Source code
.use_names_to_integer_indices 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 Source code
addPerFeatureQC Man page Source code
aggregateAcrossCells Man page
aggregateAcrossCells,SingleCellExperiment-method Man page
aggregateAcrossCells,SummarizedExperiment-method Man page
aggregateAcrossFeatures Man page Source code
annotateBMFeatures Man page Source code
bootstraps Man page
bootstraps,SingleCellExperiment-method Man page
bootstraps<- Man page
bootstraps<-,SingleCellExperiment,array-method Man page
calculateAverage Man page
calculateAverage,ANY-method Man page
calculateAverage,SingleCellExperiment-method Man page
calculateAverage,SummarizedExperiment-method Man page
calculateCPM Man page
calculateCPM,ANY-method Man page
calculateCPM,SingleCellExperiment-method Man page
calculateCPM,SummarizedExperiment-method Man page
calculateDiffusionMap Man page
calculateDiffusionMap,ANY-method Man page
calculateDiffusionMap,SingleCellExperiment-method Man page
calculateDiffusionMap,SummarizedExperiment-method Man page
calculateFPKM Man page Source code
calculateMDS Man page
calculateMDS,ANY-method Man page
calculateMDS,SingleCellExperiment-method Man page
calculateMDS,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
calculateTPM,ANY-method Man page
calculateTPM,SingleCellExperiment-method Man page
calculateTPM,SummarizedExperiment-method 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 Source code
computeMedianFactors Man page Source code
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 Source code
librarySizeFactors Man page
librarySizeFactors,ANY-method Man page
librarySizeFactors,SummarizedExperiment-method Man page
logNormCounts Man page
logNormCounts,SingleCellExperiment-method Man page
logNormCounts,SummarizedExperiment-method Man page
makePerCellDF Man page Source code
makePerFeatureDF Man page Source code
medianSizeFactors Man page
medianSizeFactors,ANY-method Man page
medianSizeFactors,SummarizedExperiment-method Man page
mockSCE Man page Source code
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
normalizeCounts,ANY-method Man page
normalizeCounts,SingleCellExperiment-method Man page
normalizeCounts,SummarizedExperiment-method Man page
numDetectedAcrossCells Man page
numDetectedAcrossCells,ANY-method Man page
numDetectedAcrossCells,SummarizedExperiment-method Man page
numDetectedAcrossFeatures Man page
numDetectedAcrossFeatures,ANY-method Man page
numDetectedAcrossFeatures,SummarizedExperiment-method Man page
paired_reddim_plot Source code
perCellQCMetrics Man page
perCellQCMetrics,ANY-method Man page
perCellQCMetrics,SingleCellExperiment-method Man page
perCellQCMetrics,SummarizedExperiment-method Man page
perFeatureQCMetrics Man page
perFeatureQCMetrics,ANY-method Man page
perFeatureQCMetrics,SummarizedExperiment-method Man page
per_cell_qc Source code
per_feature_qc Source code
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
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 Source code
readSparseCounts Man page Source code
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
sc_example_cell_info Man page
sc_example_counts Man page
scater-plot-args Man page
scater-utils 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
sumCountsAcrossCells,ANY-method Man page
sumCountsAcrossCells,SummarizedExperiment-method Man page
sumCountsAcrossFeatures Man page
sumCountsAcrossFeatures,ANY-method Man page
sumCountsAcrossFeatures,SummarizedExperiment-method Man page
sum_row_counts Source code
toSingleCellExperiment Man page Source code
top_cumprop Source code
uniquifyFeatureNames Man page Source code
updateSCESet Man page Source code
scater documentation built on June 28, 2020, 2 a.m.