Comments (1)
The latest update to the package should allow you to load cellranger v3 output with the load10X
function as before. I'm not really sure what you are referring to with Seurat V3. The output of SoupX is a corrected sparse matrix which can be loaded into any downstream analysis package, including any version of Seurat, instead of the uncorrected input.
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Related Issues (20)
- Error running SoupX HOT 2
- For loops don't seem to work with soupX
- Error: No plausible marker genes found
- Unable to knit when running load10X from SoupX
- table of droplets (tod) and table of counts (toc) have different numbers of genes HOT 10
- Combining Ambient RNA Methods
- Conflicting SoupX results
- Extremely high contamination estimated (0.61)
- RNA velocity HOT 1
- Running SoupX on Multiome Data
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- Manually setting contamination fraction
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- plotMarkerMap returns empty plot
- Error converted from warning HOT 1
- SoupX error
- tar.gz cellranger folders
- Donor specific ambient RNA
- Correction of ADT tags (protein data) of CITEseq
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from soupx.