Man pages for SoupX
Single Cell mRNA Soup eXterminator
| adjustCounts | Remove background contamination from count matrix |
| alloc | Allocate values to "buckets" subject to weights and... |
| autoEstCont | Automatically calculate the contamination fraction |
| calculateContaminationFraction | Calculate the contamination fraction |
| estimateNonExpressingCells | Calculate which cells genuinely do not express a particular... |
| estimateSoup | Get expression profile of soup |
| expandClusters | Expands soup counts calculated at the cluster level to the... |
| 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... |
| plotMarkerMap | Plot ratio of observed to expected counts on reduced... |
| plotSoupCorrelation | Plot correlation of expression profiles of soup and... |
| 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... |
