https://github.com/gyorilab/neuroimmune_interactome
https://github.com/gyorilab/neuroimmune_interactome
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/gyorilab/neuroimmune_interactome
- Owner: gyorilab
- Created: 2022-11-07T15:26:15.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2024-05-13T18:44:58.000Z (about 1 year ago)
- Last Synced: 2024-11-17T12:19:52.611Z (6 months ago)
- Language: HTML
- Size: 23.1 MB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# Neuro-immune interactome
This repository accompanies the manuscript "Nociceptor neuroimmune interactomes
reveal common and injury-specific inflammatory pain pathways" and contains
code to generate the interactome.
The Python script to generate the interactome is at `interactome/core.py`.
Output files, including gene lists and generated CellPhoneDB input interaction tables
are in the `output` folder.
In the `output/cpdb` folder, interactome files
using UniProt IDs are provided:
- `ligand_receptor_unique_interactions.csv`
- `ligand_ion_channel_interactions.csv`
- `enzyme_product_unique_interactions.csv`
which are used as input to CellPhoneDB. In addition, versions of these
interactome files that use gene names
- `enzyme_product_unique_interactions_hgnc.csv`
- `ligand_ion_channel_unique_interactions_hgnc.csv`
- `ligand_receptor_unique_interactions_hgnc.csv`
are also provided for convenience. Finally, the merged interactome is available
both using UniProt IDs and using gene names:
- `all_interactions.csv`
- `all_interactions_hgnc.csv`