PBMC_metaData           PBMC 4K meta data
PBMC_sc                 SoupChannel from PBMC data
SoupChannel             Construct a SoupChannel object
SoupX                   SoupX: Profile, quantify and remove ambient RNA
                        expression from droplet based RNA-seq
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
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
