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Katsevich-Lab / sceptre

An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.
https://katsevich-lab.github.io/sceptre/
GNU General Public License v3.0
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Option to add cells with 0 counts for the target in run_qc() #110

Closed redbybeing closed 4 months ago

redbybeing commented 5 months ago

Hi!

As far as I understand, in QC step, for a given gene-gRNA pair, sceptre removes cells (both ctrl & perturbed) where the target gene count is 0. Our team found that for our dataset, there is a great need for including cells with 0 counts for the target gene in run_qc(). Is there an easy way to do that?

Thank you so much!

Best, Jiseok

timothy-barry commented 5 months ago

Hi Jiseok,

Would you mind adding this question to the Discussion page? We are trying to reserve issues for bugs.