bpuzek

large number of doublets and AMB calls with demuxlet

1

We are trying to run demuxlet with 8 individuals, using the suggested `--alpha 0 --alpha 0.5` parameters We are getting 82% ambiguous calls, 13% doublets and 5% singlets. As discussed...

souporcell3

3

Dear developers, I saw that there is now souporcell3 (https://www.biorxiv.org/content/10.1101/2025.07.10.664218v1) developed for larger number of donors. Does the code in this repo correspond to souporcell3? Best, Barbara

Ambient RNA estimation

1

Dear developers, thank you for the amazing tool. I want to make use of the ambient RNA proportion estimates. I am trying to find those in prop_ambient.tsv output files, but...