Man pages for constantAmateur/SoupX
Single cell mRNA Soup eXterminator

adjustCountsAdjust counts to remove soup
calculateContaminationFractionCalculate the contamination fraction
createCleanedSeuratConvert multiple strained channels into a Seurat object
estGroupedEstimates contamination from a group of cells
estimateSoupGet expression profile of soup
estRateLimsCalculate limits on estimated binomial rate from data
findCellsEstimates which droplets contain a cell
identifyExpressingCellsIdentify expressing cells
inferNonExpressedGenesCalculates the genes most likely to be non-expressed in some...
interpolateCellContaminationGet cell specific rho from binned values
load10XLoad a collection of 10X data-sets
PBMC_DRtSNE coordinates for PBMC data
PBMC_SCLBasic Soup Channel List for PBMC data
plotCandidateMarkerGenesPlot non-expressed genes for channel
plotChangeMapPlot maps comparing corrected/raw expression
plotChannelContaminationPlot contamination fraction for channel
plotMarkerDistributionPlots the distribution of the observed to expected expression...
plotMarkerMapPlot ratio of observed to expected counts on reduced...
plotSoupCorrelationPlot correlation of expression profiles of soup and...
print.SoupChannelPrint method for SoupChannel
print.SoupChannelListPrint method for SoupChannelList
quickMarkersGets top N markers for each cluster
SoupChannelConstruct a SoupChannel object
SoupChannelListConstruct a SoupChannelList object
SoupXSoupX: Profile, quantify and remove ambient RNA expression...
strainCellsRemove background contamination from cell expression profile
constantAmateur/SoupX documentation built on June 26, 2018, 10:19 a.m.