https://github.com/compomics/oui-discovery
Collaboration between CompOmics & OpenProt group
https://github.com/compomics/oui-discovery
Last synced: about 2 months ago
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Collaboration between CompOmics & OpenProt group
- Host: GitHub
- URL: https://github.com/compomics/oui-discovery
- Owner: CompOmics
- License: apache-2.0
- Created: 2025-06-26T13:48:09.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2025-12-19T18:50:30.000Z (3 months ago)
- Last Synced: 2025-12-22T08:02:16.591Z (3 months ago)
- Language: Jupyter Notebook
- Size: 220 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
This repository contains code for publication [DOI].
Input data is on Zenodo: 10.5281/zenodo.18023698
To reproduce the entrapment analysis: https://github.com/Labo-MAB/Ionbot_FDP/tree/tpp-fragpipe-ranks-groupwalk
TPP and FragPipe parameters (oui-discovery-vv): tpp_run/ & fragpipe_run/
Figures in .svg: publication-data/Final-figures/
Panels for figures 1-5 & 8-10: oui-discovery-vv-plot/
### To reproduce figures
**f1** oui-discovery-vv/: plot-0-fdp.ipynb
**f2-3** oui-discovery-vv/: explore-1-tpp-1-preprocess.ipynb → do-0-protein-inference-tpp-fragpipe.ipynb & explore-1-tpp-2-stats.ipynb; explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-closed-2-stats.ipynb; compare-2-tpp-ionbot-closed.ipynb
**f4-5** oui-discovery-vv/: explore-1-fragpipe-1-preprocess.ipynb → do-0-protein-inference-tpp-fragpipe.ipynb & explore-1-fragpipe-2-stats.ipynb; explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb; compare-2-fragpipe-ionbot-open.ipynb
**f6**: Comparison-4-new-Sankey-global.ipynb & Comparison-5-ionbot-features-tr-combo-global.ipynb
**f7**: Comparison-6b-open-vs-closed-search-global.ipynb
**f8** oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb
**f9** oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb & explore-1-ionbot-closed-2-stats.ipynb → compare-2-ionbot-closed-open.ipynb
**f10** oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb → explore-3-ionbot-open-noncanon-hpp.ipynb & explore-3-ionbot-open-noncanon-spectra.ipynb
**fs1-2** oui-discovery-vv/: plot-0-fdr-vs-ranks.ipynb
**fs3**: see f2-5
**fs4**: see f10