Gaux Wang
Gaux Wang
I met the same problem and reverting to the previous version can fix. thanks
I had the same problem and how did you solve it? thanks!
Actually I don't know if "variant fraction" means "Count of observations of this alternate / All read counts", and if that's right, the variant fraction of "chr4 5742730" site should...
Varscan2 doesn't report anything in the site..ðŸ˜
it doesn't work
raw data: https://www.ncbi.nlm.nih.gov/sra?term=SRX2914406 slamdunk version: slamdunk 0.4.3 And actually I have tried bcftools and freebayes, both of them can't call this site.
Hi, same confusion here. According to: https://github.com/scverse/scanpy/issues/969#issuecomment-629667682 If I set `flavor ='cell_ranger'`, dose it mean I should not use `sc.pp.log1p(adata)` to ensure use the "library size normalized counts"(not log)?
@DelongZHOU `FindDMEs()` will create a new assay to reuse `Seurat::FindMarkers()`. In your case, `L6_CT-M2` is illegal for Seurat(underscores ('_')), which cause `PlotDMEsVolcano()` receive wrong module names.
Any updates?
I had the same problem, I must downgrade numpy to 1.26