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phydms

phylogenetic analyses informed by deep mutational scanning data

https://github.com/jbloomlab/phydms

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 5 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.8%) to scientific vocabulary

Keywords

deep-mutational-scanning molecular-evolution phylogenetics protein-evolution
Last synced: 6 months ago · JSON representation

Repository

phylogenetic analyses informed by deep mutational scanning data

Basic Info
  • Host: GitHub
  • Owner: jbloomlab
  • License: gpl-3.0
  • Language: HTML
  • Default Branch: master
  • Size: 14.9 MB
Statistics
  • Stars: 15
  • Watchers: 4
  • Forks: 5
  • Open Issues: 5
  • Releases: 0
Topics
deep-mutational-scanning molecular-evolution phylogenetics protein-evolution
Created over 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.rst 

========================
``phydms``
========================
.. image:: https://travis-ci.org/jbloomlab/phydms.svg?branch=master
    :target: https://travis-ci.org/jbloomlab/phydms

``phydms`` enables **phy**\logenetic analyses using **d**\eep **m**\utational **s**\canning data to inform the substitution models. It implements **Exp**\erimentally informed **c**\odon **m**\odels (*ExpCM*) for phylogenetic inference and the detection of biologically interesting selection.

``phydms`` is written by the `Bloom lab`_ (see https://github.com/jbloomlab/phydms/contributors for a full list of contributors).

See the `phydms documentation`_ for information about using ``phydms`` and details about the recommended installation process.

The `phydms source code`_ is freely available under a `GPLv3`_ license.

If you use ``phydms``, please `cite it appropriately`_.


.. _`Jesse Bloom`: http://research.fhcrc.org/bloom/en.html
.. _`phydms documentation`: http://jbloomlab.github.io/phydms/
.. _`phydms source code`: https://github.com/jbloomlab/phydms
.. _`GPLv3`: http://www.gnu.org/copyleft/gpl.html
.. _`Bloom lab`: http://labs.fhcrc.org/bloom
.. _`cite it appropriately`: http://jbloomlab.github.io/phydms/acknowledgments.html

Owner

  • Name: jbloomlab
  • Login: jbloomlab
  • Kind: organization
  • Email: jbloom@fredhutch.org
  • Location: Seattle, WA, USA

Jesse Bloom's lab GitHub account

GitHub Events

Total
  • Issue comment event: 1
  • Member event: 2
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Issue comment event: 1
  • Member event: 2
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 928
  • Total Committers: 5
  • Avg Commits per committer: 185.6
  • Development Distribution Score (DDS): 0.598
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
jbloom j****m@f****g 373
Sarah Hilton s****n@u****u 327
jbloom j****m@f****g 223
Michael Doud m****d@u****u 4
adingens a****s@u****u 1
Committer Domains (Top 20 + Academic)
uw.edu: 3 fhcrc.org: 1 fredhutch.org: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 26
  • Total pull requests: 22
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 15 hours
  • Total issue authors: 10
  • Total pull request authors: 5
  • Average comments per issue: 1.85
  • Average comments per pull request: 0.86
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: 7 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • skhilton (8)
  • jbloom (7)
  • mbdoud (3)
  • gavinmdouglas (2)
  • mokiine (1)
  • SternLabTAU (1)
  • kevinmyers (1)
  • cahuparo (1)
  • jiroop (1)
  • Hamil462 (1)
Pull Request Authors
  • jbloom (8)
  • skhilton (7)
  • jon-mah (5)
  • davidrich27 (2)
  • gavinmdouglas (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 57 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 36
  • Total maintainers: 1
pypi.org: phydms

Phylogenetic analyses informed by deep mutational scanning data.

  • Versions: 36
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 57 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Average: 14.2%
Stargazers count: 16.5%
Forks count: 16.8%
Downloads: 18.6%
Maintainers (1)
jbloom
Last synced: 7 months ago

Dependencies

setup.py pypi
  • PyPDF2 >=1.26
  • biopython >=1.67
  • cython >=0.28
  • matplotlib >=2.0.2
  • natsort >=5.0.1
  • numpy >=1.16.5
  • pandas >=0.20.2
  • pyvolve >=1.0.3
  • scipy >=0.18
  • six >=1.10
  • statsmodels >=0.8
  • sympy >=1.0
  • weblogo >=3.4,
test_requirements.txt pypi
  • flake8 * test
  • flake8-bugbear * test
  • flake8-builtins * test
  • flake8-comprehensions * test
  • flake8-docstrings * test
  • flake8-import-order * test
  • flake8-per-file-ignores * test
  • flake8-print * test
  • flake8-rst-docstrings * test
  • pytest * test