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 |