https://github.com/andim/pyrepseq
Python library for immune repertoire analysis
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (18.4%) to scientific vocabulary
Repository
Python library for immune repertoire analysis
Basic Info
- Host: GitHub
- Owner: andim
- License: mit
- Language: Python
- Default Branch: main
- Size: 529 KB
Statistics
- Stars: 16
- Watchers: 8
- Forks: 4
- Open Issues: 10
- Releases: 15
Metadata Files
README.md
Pyrepseq: the immune repertoire analysis toolkit
Pyrepseq is scipy & seaborn for studying adaptive immunity: modular implementations of algorithms for fast analyses, and bespoke plotting functions for compelling visualizations.
Documentation and examples
You can find API documentation on readthedocs. You can also create a local copy of the API documentation by running:
bash
make html
in the docs folder.
There are jupyter notebooks illustrating some of the functionality in the 'examples' folder. You can also find usage examples by looking at the code underlying our recent paper Mayer Callan PNAS 2023.
Installation
The quickest way to install Pyrepseq is via pip:
bash
pip install pyrepseq[full]
This will install pyrepseq with all optional dependencies. Depending on whether dependencies are already installed this might take a few minutes. You can also install the leading edge development version using:
bash
pip install git+https://github.com/andim/pyrepseq
As the TCRdist dependency on parasail is known to cause installation issues on Mac OSX, pyrepseq can also be installed without this dependency by running:
bash
pip install pyrepseq
In this case some functionality will not be available. To allow installation to proceed on mac you might have to manually install build tools using:
bash
brew install autoconf automake libtool
Pyrepseq can also be installed from its Github source, by running:
bash
python setup.py install
in the main directory.
Support and contributing
For bug reports and enhancement requests use the Github issue tool, or (even better!) open a pull request with relevant changes. If you have any questions don't hesitate to contact us by email (andimscience@gmail.com) or Twitter (@andimscience).
You can run the testsuite by running pytest in the top-level directory.
Dependencies for generating testing and generating local versions of the documentation can be installed using:
bash
pip install pyrepseq[dev]
You are cordially invited to contribute to the further development of pyrepseq!
Owner
- Name: Andreas Tiffeau-Mayer
- Login: andim
- Kind: user
- Location: London
- Company: University College London
- Website: https://andim.github.io/
- Twitter: andimscience
- Repositories: 26
- Profile: https://github.com/andim
Quantitative Immunology, Biological Physics
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Push event: 5
- Create event: 1
Last Year
- Issues event: 1
- Watch event: 1
- Push event: 5
- Create event: 1
Packages
- Total packages: 1
-
Total downloads:
- pypi 197 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 14
- Total maintainers: 1
pypi.org: pyrepseq
Python library for immune repertoire analyses
- Homepage: http://pyrepseq.readthedocs.io/
- Documentation: https://pyrepseq.readthedocs.io/
- License: MIT
-
Latest release: 1.5.1
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- Levenshtein *
- matplotlib *
- numpy *
- pandas *
- scipy *
- seaborn *
- actions/checkout v3 composite
- actions/setup-python v3 composite
- pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite