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@biocommons

biocommons

a collection of open source bioinformatics tools
README.md

The biocommons is a community that fosters collaboration on pre-competitive, interoperable, and high-quality bioinformatics open source software and data, primarily for biological sequence analysis and interpretation.

Code is released under Apache License v2 and data are released under the Creative Commons CC-BY 4.0 license.

See biocommons.org for more information.

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  1. hgvs hgvs Public

    Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

    Python 294 103

  2. uta uta Public

    Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

    Python 73 27

  3. bioutils bioutils Public

    provides common tools and lookup tables used primarily by the hgvs and uta packages

    Python 25 22

  4. biocommons.seqrepo biocommons.seqrepo Public

    non-redundant, compressed, journalled, file-based storage for biological sequences

    Python 52 36

  5. eutils eutils Public archive

    simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

    Python 63 29

  6. seqrepo-rest-service seqrepo-rest-service Public

    OpenAPI-based REST interface to biological sequences and sequence metadata

    Python 6 6

Repositories

Showing 10 of 25 repositories
  • github-stats Public

    GitHub repository statistics collection for biocommons repositories

    biocommons/github-stats's past year of commit activity
    Vue 0 0 0 0 Updated Oct 21, 2026
  • python-package Public template

    Template for new biocommons packages, and source of configuration for periodic updates to derived packages

    biocommons/python-package's past year of commit activity
    Makefile 1 Apache-2.0 2 5 2 Updated Oct 21, 2026
  • hgvs Public

    Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

    biocommons/hgvs's past year of commit activity
    Python 294 Apache-2.0 103 28 10 Updated Oct 21, 2026
  • biocommons.seqrepo Public

    non-redundant, compressed, journalled, file-based storage for biological sequences

    biocommons/biocommons.seqrepo's past year of commit activity
    Python 52 Apache-2.0 36 13 3 Updated Oct 21, 2026
  • spike-dependabot-automerge Public

    TEMPORARY spike for biocommons/infra#7; will be deleted

    biocommons/spike-dependabot-automerge's past year of commit activity
    0 0 0 1 Updated Oct 19, 2026
  • bioutils Public

    provides common tools and lookup tables used primarily by the hgvs and uta packages

    biocommons/bioutils's past year of commit activity
    Python 25 Apache-2.0 22 3 5 Updated Oct 19, 2026
  • anyvar Public

    Lightweight, portable variation registration and retrieval

    biocommons/anyvar's past year of commit activity
    Python 17 Apache-2.0 6 34 2 Updated Oct 16, 2026
  • biocommons.github.io Public

    biocommons website, deployed to Read the Docs

    biocommons/biocommons.github.io's past year of commit activity
    Python 1 Apache-2.0 2 3 0 Updated Oct 13, 2026
  • .github Public

    Organization-wide GitHub configuration

    biocommons/.github's past year of commit activity
    2 0 2 0 Updated Oct 12, 2026
  • uta Public

    Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

    biocommons/uta's past year of commit activity
    Python 73 Apache-2.0 27 27 1 Updated Jun 27, 2026
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