# Single Cell mRNA Soup eXterminator

## Documentation for package ‘SoupX’ version 1.4.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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