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scikit-allel

A Python package for exploring and analysing genetic variation data

https://github.com/cggh/scikit-allel

Science Score: 46.0%

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
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    4 of 13 committers (30.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary

Keywords from Contributors

genomics bioinformatics coalescent genetics msprime trees tskit
Last synced: 7 months ago · JSON representation

Repository

A Python package for exploring and analysing genetic variation data

Basic Info
  • Host: GitHub
  • Owner: cggh
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 38.2 MB
Statistics
  • Stars: 299
  • Watchers: 25
  • Forks: 54
  • Open Issues: 115
  • Releases: 45
Created about 11 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.rst 

``scikit-allel``
================

A Python package for exploratory analysis of large scale genetic variation data.

* Documentation: http://scikit-allel.readthedocs.org
* Source code: https://github.com/cggh/scikit-allel
* Download: https://pypi.python.org/pypi/scikit-allel

.. image:: https://zenodo.org/badge/7890/cggh/scikit-allel.svg
   :target: https://zenodo.org/badge/latestdoi/7890/cggh/scikit-allel

.. image:: https://readthedocs.org/projects/scikit-allel/badge/?version=latest
    :target: http://scikit-allel.readthedocs.io/en/latest/?badge=latest

.. image:: https://travis-ci.org/cggh/scikit-allel.svg?branch=master
    :target: https://travis-ci.org/cggh/scikit-allel

.. image:: https://ci.appveyor.com/api/projects/status/1fna2yr9uht0u296?svg=true
    :target: https://ci.appveyor.com/project/alimanfoo/scikit-allel


Development status
******************

Please note that scikit-allel is no longer under active development
and is now in "maintenance-only" mode. The intended successor
project is `sgkit `__ (the Statistical
Genetics Toolkit) which should support all the functionality of sckit-allel,
but provide better scaling, performance and maintainability.
Sgkit is not yet at feature parity with scikit-allel and is therefore
not ready for all applications, but we welcome `contributions
`__!

Owner

  • Name: Centre for Genomics and Global Health
  • Login: cggh
  • Kind: organization
  • Email: info@cggh.org

GitHub Events

Total
  • Watch event: 12
  • Delete event: 5
  • Issue comment event: 10
  • Push event: 117
  • Pull request event: 16
  • Fork event: 3
  • Create event: 9
Last Year
  • Watch event: 12
  • Delete event: 5
  • Issue comment event: 10
  • Push event: 117
  • Pull request event: 16
  • Fork event: 3
  • Create event: 9

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 898
  • Total Committers: 13
  • Avg Commits per committer: 69.077
  • Development Distribution Score (DDS): 0.058
Past Year
  • Commits: 5
  • Committers: 3
  • Avg Commits per committer: 1.667
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
Alistair Miles a****o@g****m 846
pyup-bot g****t@p****o 32
Nick Harding n****h@w****k 9
Murillo F. Rodrigues m****s@g****m 2
nhaseley n****y@i****m 1
Jerome Kelleher jk@w****k 1
Murillo Rodrigues m****s@K****l 1
Nick Harding n****g@b****k 1
Rahul Pisupati r****i@g****t 1
Max Schelker m****r@g****m 1
peter p****p@g****m 1
Tim Millar t****r 1
Summer Rae s****a 1
Committer Domains (Top 20 + Academic)
well.ox.ac.uk: 2 gmx.com: 1 gmi.oeaw.ac.at: 1 bdi.ox.ac.uk: 1 illumina.com: 1 pyup.io: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 57
  • Total pull requests: 125
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 46
  • Total pull request authors: 15
  • Average comments per issue: 2.47
  • Average comments per pull request: 1.23
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 3
  • Pull requests: 29
  • Average time to close issues: about 7 hours
  • Average time to close pull requests: 25 days
  • Issue authors: 2
  • Pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.76
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • alimanfoo (8)
  • mufernando (3)
  • vsbuffalo (2)
  • travc (2)
  • kullrich (1)
  • schimar (1)
  • NTNguyen13 (1)
  • KazegamiKuon (1)
  • timothymillar (1)
  • grlewis333 (1)
  • pengyan19 (1)
  • crisamor (1)
  • Hjorvik (1)
  • tomwells-oxf (1)
  • tiagoantao (1)
Pull Request Authors
  • pyup-bot (80)
  • alimanfoo (17)
  • dependabot[bot] (6)
  • hardingnj (3)
  • leshaker (3)
  • timothymillar (3)
  • benjeffery (2)
  • maxibor (2)
  • mufernando (2)
  • sanjaynagi (2)
  • smbadiwe (1)
  • yakkoroma (1)
  • olavurmortensen (1)
  • jeromekelleher (1)
  • andrewgwalker (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (6) github_actions (2)

Dependencies

requirements.txt pypi
  • cython *
  • dask *
  • h5py *
  • hmmlearn *
  • ipython *
  • matplotlib *
  • numcodecs *
  • numexpr *
  • numpy *
  • pandas *
  • pomegranate *
  • pytest *
  • scikit-learn *
  • scipy *
  • seaborn *
  • zarr *
requirements_dev_base.txt pypi
  • cython ==0.29.24 development
  • dask ==2021.9.1 development
  • numpy ==1.21.2 development
requirements_dev_optional.txt pypi
  • h5py ==3.4.0 development
  • hmmlearn ==0.2.6 development
  • ipython ==7.28.0 development
  • matplotlib ==3.4.3 development
  • numexpr ==2.7.3 development
  • pandas ==1.3.3 development
  • pomegranate ==0.14.5 development
  • pyfasta ==0.5.2 development
  • scikit-learn ==1.0 development
  • scipy ==1.7.1 development
  • seaborn ==0.11.2 development
  • zarr ==2.10.1 development
requirements_rtfd.txt pypi
  • mock *
  • numpy *
  • numpydoc *
  • sphinx *
  • sphinx-issues *
requirements_test.txt pypi
  • coverage * test
  • coveralls * test
  • flake8 * test
  • pytest * test
  • pytest-cov * test
  • setuptools * test
  • setuptools-scm * test
  • tox * test
.github/workflows/deploy.yml actions
  • actions/checkout v2 composite
  • actions/download-artifact v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
  • joerick/cibuildwheel v1.11.0 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/test.yml actions
  • actions/checkout v1 composite
  • actions/setup-python v2 composite
pyproject.toml pypi
setup.py pypi