Include all genes in copykat_CNA_raw_results_gene_by_cell.txt.

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
42/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
r
Domain
bioinformatics

Research direction

Start by locating where copykat_CNA_raw_results_gene_by_cell.txt is generated and where genes are filtered. Check how expressed genes such as YC and CCND1 are handled, then verify that the output includes all requested genes rather than only the filtered subset.

Written by the indexing model from the issue text.

Description

Hi,
Thanks for the amazing tool! Was wondering if I could get CNV profiles of all genes in the copykat_CNA_raw_results_gene_by_cell.txt. A lot of genes are filtered out - even the ones like YC, CCND1 that are expressed abundantly. It would be great if you could help me with this.

Thanks,
Prakrithi

Dominant language
R
Stars
305
Forks
66
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