| 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 |