https://github.com/bzhanglab/xlranker
prioritization tool for ppi-xl data
Science Score: 26.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.8%) to scientific vocabulary
Keywords
Repository
prioritization tool for ppi-xl data
Basic Info
- Host: GitHub
- Owner: bzhanglab
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://bzhanglab.github.io/xlranker/
- Size: 42.2 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
XLRanker
<!-- Badges -->
XLRanker is a tool to rank and prioritize protein to protein cross linking data. The tool uses parsimonious selection as well as an XGBoost model to select the best protein pairs to represent ambiguous peptides.
Installation
You can install xlranker using pip:
bash
pip install xlranker
Usage
To analyze a TSV file containing a network of peptide sequences run:
xlranker start peptide_network.tsv
Please view the documentation for detailed usage instructions and examples.
Example Notebook
For a quick start, you can check out the example notebook in the notebooks directory or launch a google colab notebook to see how to use the package interactively.
Owner
- Name: Zhang Lab
- Login: bzhanglab
- Kind: organization
- Location: Houston, TX
- Website: https://www.zhang-lab.org
- Repositories: 15
- Profile: https://github.com/bzhanglab
Translating omics data into biological insights.
GitHub Events
Total
- Release event: 3
- Delete event: 8
- Public event: 1
- Push event: 40
- Pull request event: 12
- Create event: 11
Last Year
- Release event: 3
- Delete event: 8
- Public event: 1
- Push event: 40
- Pull request event: 12
- Create event: 11
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 34
- Average time to close issues: N/A
- Average time to close pull requests: 3 minutes
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 34
- Average time to close issues: N/A
- Average time to close pull requests: 3 minutes
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- iblacksand (34)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 28 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
pypi.org: xlranker
PPI-XL Ranking Tool
- Documentation: https://xlranker.readthedocs.io/
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Latest release: 0.2.1
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v4 composite
- astral-sh/setup-uv v5 composite
- actions/checkout v4 composite
- astral-sh/setup-uv v5 composite
- biopython >=1.85
- cyclopts >=3.15.0
- networkx >=3.4.2
- polars >=1.29.0
- questionary >=2.1.0
- scikit-learn >=1.6.1
- xgboost >=3.0.0
- 109 dependencies