Single Cell mRNA Soup eXterminator

Documentation for package ‘SoupX’ version 1.6.2

adjustCounts	Remove background contamination from count matrix
alloc	Allocate values to "buckets" subject to weights and constraints
autoEstCont	Automatically calculate the contamination fraction
calculateContaminationFraction	Calculate the contamination fraction
estimateNonExpressingCells	Calculate which cells genuinely do not express a particular gene or set of genes
estimateSoup	Get expression profile of soup
expandClusters	Expands soup counts calculated at the cluster level to the cell level
initProgBar	Create Seurat style progress bar
load10X	Load a collection of 10X data-sets
PBMC_metaData	PBMC 4K meta data
PBMC_sc	SoupChannel from PBMC data
plotChangeMap	Plot maps comparing corrected/raw expression
plotMarkerDistribution	Plots the distribution of the observed to expected expression for marker genes
plotMarkerMap	Plot ratio of observed to expected counts on reduced dimension map
plotSoupCorrelation	Plot correlation of expression profiles of soup and aggregated cells
print.SoupChannel	Print method for SoupChannel
quickMarkers	Gets top N markers for each cluster
scToy	Toy SoupChanel object
setClusters	Sets clustering for SoupChannel
setContaminationFraction	Manually set contamination fraction
setDR	Manually set dimension reduction for a channel
setSoupProfile	Set soup profile
SoupChannel	Construct a SoupChannel object
SoupX	SoupX: Profile, quantify and remove ambient RNA expression from droplet based RNA-seq