bedapub / bedapub/besca

Add missing gene Ly6g and revise MGItoHGNC.csv

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#156 1 comment 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
Python
Stars
50
Forks
17
Avg merge
1d 4h
Merged PRs (30d)
3

Description

Hi,

Ly6g is a good mouse neutrophil marker (therefore probably will be included in the gmt file neutrophil signature).
I noticed that this gene is missing in besca/datasets/homologs/MGItoHGNC.csv and therefore exluded when computing the signatures with conversion

```
bc.tl.sig.combined_signature_score(adata, gmt_file, conversion=conversion)
```

I am also wondering if other relevant genes are lost during this conversion step. Therefore would be nice to include a print step in the function to indicate the excluded genes for revision.

Thanks,
Llucia

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with besca/datasets/homologs/MGItoHGNC.csv and the implementation of bc.tl.sig.combined_signature_score, focusing on how the conversion mapping excludes genes. Confirm how Ly6g is represented in the mapping and inspect the signature conversion path. Done means Ly6g is retained and the function reports genes excluded during conversion for review.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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