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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 Public

    Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

    Python 255 95

  2. uta Public

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

    Python 63 25

  3. bioutils Public

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

    Python 22 18

  4. biocommons.seqrepo Public

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

    Python 40 34

  5. eutils Public

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

    Python 59 26

  6. seqrepo-rest-service Public

    OpenAPI-based REST interface to biological sequences and sequence metadata

    Python 4 5

Repositories

Showing 10 of 20 repositories
  • anyvar Public

    [in development] Proof-of-Concept variation translation, validation, and registration service

    Python 13 Apache-2.0 5 8 2 Updated Mar 6, 2025
  • hgvs Public

    Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

    Python 255 Apache-2.0 95 48 4 Updated Mar 5, 2025
  • bioutils Public

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

    Python 22 Apache-2.0 18 2 1 Updated Mar 5, 2025
  • seqrepo-rest-service Public

    OpenAPI-based REST interface to biological sequences and sequence metadata

    Python 4 Apache-2.0 5 2 0 Updated Mar 4, 2025
  • biocommons.seqrepo Public

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

    Python 40 Apache-2.0 34 26 0 Updated Mar 4, 2025
  • uta Public

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

    Python 63 Apache-2.0 25 21 0 Updated Feb 3, 2025
  • mirrors-ncbi Public

    Makefile (of all things) to space-efficiently mirror selected NCBI resources

    Makefile 1 1 0 0 Updated Jan 7, 2025
  • biocommons.example Public template

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

    Makefile 1 Apache-2.0 2 4 0 Updated Sep 23, 2024
  • biocommons.github.io Public

    biocommons website

    Python 1 Apache-2.0 2 2 0 Updated Sep 1, 2024
  • eutils Public

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

    Python 59 Apache-2.0 26 5 0 Updated Jun 26, 2024
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