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epitopepredict

Python package and command line tool for epitope prediction

https://github.com/dmnfarrell/epitopepredict

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.4%) to scientific vocabulary

Keywords

bioinformatics epitope-prediction-methods immunology
Last synced: 10 months ago · JSON representation

Repository

Python package and command line tool for epitope prediction

Basic Info
  • Host: GitHub
  • Owner: dmnfarrell
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 24.9 MB
Statistics
  • Stars: 52
  • Watchers: 5
  • Forks: 22
  • Open Issues: 5
  • Releases: 5
Topics
bioinformatics epitope-prediction-methods immunology
Created over 11 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

PyPI version shields.io License: GPL v3 Documentation Status

Background

epitopepredict provides a standardized programmatic interface and command line tool for executing multiple epitope prediction methods. Currently this largely consists of interfaces to several MHC binding prediction, the results of which can then be processed and visualized in a consistent manner. There is a built-in method for MHC-class I prediction and the TEPITOPEPan method is provided as a 'built in' method for MHC-class II. The IEDB tools and netMHCpan, netMHCIIpan and MHCFlurry are also supported. Those tools are free for academic use but have to be installed separately. This software runs on most linux systems.

Documentation is at http://epitopepredict.readthedocs.io

Installation

current release:

pip install epitopepredict

or for latest version on github:

pip install -e git+https://github.com/dmnfarrell/epitopepredict.git#egg=epitopepredict

Owner

  • Name: Damien Farrell
  • Login: dmnfarrell
  • Kind: user
  • Location: Dublin, Ireland
  • Company: University College Dublin

Research Fellow UCD Veterinary School ORCID ID: 0000-0003-3020-7945

GitHub Events

Total
  • Issues event: 3
  • Watch event: 3
  • Issue comment event: 1
Last Year
  • Issues event: 3
  • Watch event: 3
  • Issue comment event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 278
  • Total Committers: 4
  • Avg Commits per committer: 69.5
  • Development Distribution Score (DDS): 0.022
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Damien Farrell f****n@g****m 272
dmnfarrell f****l@b****e 4
Taeyoon Kim p****a 1
Nokome Bentley n****e@s****a 1
Committer Domains (Top 20 + Academic)
stenci.la: 1 bola.ucd.ie: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 11
  • Total pull requests: 3
  • Average time to close issues: 21 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 10
  • Total pull request authors: 3
  • Average comments per issue: 1.64
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • partrita (2)
  • berkedilekoglu (1)
  • chumawinnie (1)
  • jasonzhao0307 (1)
  • ever4cyth (1)
  • wt12318 (1)
  • carlomazzaferro (1)
  • pedromachadorodri (1)
  • christelvanharen (1)
  • francescopatane96 (1)
Pull Request Authors
  • wt12318 (1)
  • nokome (1)
  • partrita (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 43 last-month
  • Total docker downloads: 90
  • Total dependent packages: 1
  • Total dependent repositories: 4
  • Total versions: 5
  • Total maintainers: 1
pypi.org: epitopepredict

Python package for epitope prediction

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 4
  • Downloads: 43 Last month
  • Docker Downloads: 90
Rankings
Docker downloads count: 2.8%
Dependent packages count: 4.7%
Dependent repos count: 7.5%
Forks count: 8.2%
Average: 8.9%
Stargazers count: 9.9%
Downloads: 20.4%
Maintainers (1)
damienfa
Last synced: 11 months ago

Dependencies

doc/requirements.txt pypi
  • biopython *
  • bokeh *
  • future *
  • matplotlib *
  • numpy *
  • pandas *
requirements.txt pypi
  • biopython *
  • matplotlib *
  • mhcflurry *
  • numpy *
  • pandas *
  • seaborn *
setup.py pypi
  • biopython >=1.78
  • future *
  • joblib >=0.16.0
  • matplotlib *
  • numpy >=1.10
  • pandas >=0.22
  • scikit-learn >=0.23.2