PyGenePlexus
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krishnanlab
A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.
updates: - [github.com/asottile/reorder-python-imports: v3.12.0 → v3.14.0](https://github.com/asottile/reorder-python-imports/compare/v3.12.0...v3.14.0) - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v5.0.0) - [github.com/asottile/pyupgrade: v3.15.0 → v3.19.1](https://github.com/asottile/pyupgrade/compare/v3.15.0...v3.19.1) - [github.com/psf/black: 23.12.1 → 25.1.0](https://github.com/psf/black/compare/23.12.1...25.1.0)
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In `_get_negatives` it would be good to display what genes were considered neutrals. Possibly even which Term ID they came from and could add the neutral marker in addition to...
@billspat @jacobnewsted It might be good to have one/all of the following displayed when the validation is run, which can be taken care of in the python package 1. have...
Add a function so a user can aggregate results across different models - Does it make sense to do across different gene sets? - How to handle going across different...
Currently, to make output edgelist of the top genes, it needs to read/parse the whole edgelist. Some quick thoughts - Save edgelist files as json with node as key and...
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A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.