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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 288 97

  2. uta uta Public

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

    Python 71 25

  3. bioutils bioutils Public

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

    Python 25 20

  4. biocommons.seqrepo biocommons.seqrepo Public

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

    Python 50 35

  5. eutils eutils Public archive

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

    Python 64 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 23 repositories
  • 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 288 Apache-2.0 97 45 5 Updated Apr 17, 2026
  • anyvar Public

    Lightweight, portable variation registration and retrieval

    biocommons/anyvar’s past year of commit activity
    Python 16 Apache-2.0 6 35 3 Updated Apr 16, 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
    Python 1 Apache-2.0 2 1 1 Updated Apr 13, 2026
  • biocommons.github.io Public

    biocommons website

    biocommons/biocommons.github.io’s past year of commit activity
    Python 1 Apache-2.0 2 4 0 Updated Apr 2, 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 71 Apache-2.0 25 26 0 Updated Mar 24, 2026
  • discussions Public

    Repository for organization-wide GitHub Discussions configuration

    biocommons/discussions’s past year of commit activity
    0 0 0 0 Updated Feb 10, 2026
  • .github Public

    Organization-wide GitHub configuration

    biocommons/.github’s past year of commit activity
    2 0 0 0 Updated Feb 10, 2026
  • eutils Public archive

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

    biocommons/eutils’s past year of commit activity
    Python 64 Apache-2.0 29 1 1 Updated Feb 9, 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 20 1 0 Updated Jan 12, 2026
  • biocommons.seqrepo Public

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

    biocommons/biocommons.seqrepo’s past year of commit activity
    Python 50 Apache-2.0 35 11 0 Updated Nov 10, 2025
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