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

Global functions
GET_FUN Source code
Reduced dimension plots Man page
SCESet Man page
SCESet-class Man page
SET_FUN Source code
add_extra_guide Source code
apply_to_size_factors Source code
arrange Man page
arrange,SingleCellExperiment-method Man page
assign_jobs_to_workers Source code
bootstraps Man page
bootstraps,SingleCellExperiment-method Man page
bootstraps<- Man page
bootstraps<-,SingleCellExperiment,array-method Man page
calcAverage Man page
calculateAverage Man page Source code
calculateCPM Man page Source code
calculateFPKM Man page Source code
calculateQCMetrics Man page Source code
calculateTPM Man page Source code
cbind_overwrite_DataFrames Source code
central_plotter Source code
centreSizeFactors Man page Source code
choose_vis_values Source code
compute_averages Source code
compute_qc_metrics Source code
convert_to_full_DataFrame Source code
convert_to_nested_DataFrame Source code
create_outer_DataFrame Source code
exprs Man page
exprs,SingleCellExperiment-method, Man page
exprs<-,SingleCellExperiment,ANY-method Man page
filter Man page
filter,SingleCellExperiment-method Man page
format_per_cell Source code
format_per_feature Source code
fpkm Man page
fpkm<- Man page
getBMFeatureAnnos Man page Source code
getExplanatoryPCs Man page Source code
getVarianceExplained Man page Source code
get_all_sf_sets Source code
get_detected_per_col Source code
get_detected_per_row Source code
get_mat_for_reddim Source code
get_palette Source code
get_point_args Source code
get_thresholds Source code
isOutlier Man page Source code
librarySizeFactors Man page Source code
makePairs Source code
metadata_dispatcher Source code
multiplot Man page Source code
mutate Man page
mutate,SingleCellExperiment-method Man page
ncorporate_common_vis Source code
nexprs Man page Source code
norm_exprs Man page
norm_exprs<- Man page
normalize Man page
normalize,SingleCellExperiment-method Man page
normalizeCounts Man page Source code
normalizeSCE Man page Source code
organize_controls Source code
paired_reddim_plot Source code
plotColData Man page Source code
plotDiffusionMap Man page Source code
plotExplanatoryPCs Man page Source code
plotExplanatoryVariables Man page Source code
plotExpression Man page Source code
plotExprsFreqVsMean Man page Source code
plotExprsVsTxLength Man page Source code
plotHeatmap Man page Source code
plotHighestExprs Man page Source code
plotMDS 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
plotRLE_full Source code
plotRLE_minimal Source code
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
qc_hunter Source code
readSparseCounts Man page Source code
reddim_dispatcher Source code
rename Man page
rename,SingleCellExperiment-method Man page
replace_size_factors Source code
resolve_plot_colours Source code
rle_boxplot_stats Source code
runDiffusionMap Man page Source code
runMDS Man page Source code
runPCA Man page Source code
runTSNE Man page Source code
runUMAP Man page Source code
sc_example_cell_info Man page
sc_example_counts Man page
scale_columns Source code
scater-package Man page
scater-plot-args Man page
scater-vis-var Man page
split_vector_by_workers Source code
stand_exprs Man page
stand_exprs<- Man page
store_thresholds Source code
subset2index Source code
sumCountsAcrossFeatures Man page Source code
toSingleCellExperiment Man page Source code
uniquifyFeatureNames Man page Source code
updateSCESet Man page Source code
davismcc/scater documentation built on Dec. 12, 2018, 4:45 a.m.