Single Cell mRNA Soup eXterminator
Set soup profile
Construct a SoupChannel object
SoupX: Profile, quantify and remove ambient RNA expression from drople...
Remove background contamination from count matrix
Allocate values to "buckets" subject to weights and constraints
Automatically calculate the contamination fraction
Calculate the contamination fraction
Calculate which cells genuinely do not express a particular gene or se...
Get expression profile of soup
Expands soup counts calculated at the cluster level to the cell level
Create Seurat style progress bar
Load a collection of 10X data-sets
Plot maps comparing corrected/raw expression
Plots the distribution of the observed to expected expression for mark...
Plot ratio of observed to expected counts on reduced dimension map
Plot correlation of expression profiles of soup and aggregated cells
Print method for SoupChannel
Gets top N markers for each cluster
Sets clustering for SoupChannel
Manually set contamination fraction
Manually set dimension reduction for a channel
Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.