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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.

Pinned

  1. hgvs hgvs Public

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

    Python 232 93

  2. uta uta Public

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

    Python 60 26

  3. bioutils bioutils Public

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

    Python 18 18

  4. biocommons.seqrepo biocommons.seqrepo Public

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

    Python 39 34

  5. eutils eutils Public

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

    Python 56 26

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

    OpenAPI-based REST interface to biological sequences and sequence metadata

    Python 4 6

Repositories

Showing 10 of 20 repositories
  • biocommons.seqrepo Public

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

    Python 39 Apache-2.0 34 25 4 Updated May 27, 2024
  • hgvs Public

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

    Python 232 Apache-2.0 93 61 5 Updated May 24, 2024
  • bioutils Public

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

    Python 18 Apache-2.0 18 0 0 Updated May 24, 2024
  • biocommons.example Public template

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

    Makefile 1 1 9 2 Updated May 21, 2024
  • uta Public

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

    Python 60 Apache-2.0 26 18 0 Updated May 3, 2024
  • anyvar Public

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

    Python 11 Apache-2.0 6 10 0 Updated Apr 29, 2024
  • .github Public

    Organization-wide GitHub configuration

    1 0 0 0 Updated Apr 22, 2024
  • eutils Public

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

    Python 56 Apache-2.0 26 5 0 Updated Apr 16, 2024
  • seqrepo-rest-service Public

    OpenAPI-based REST interface to biological sequences and sequence metadata

    Python 4 Apache-2.0 6 2 1 Updated Mar 27, 2024
  • uta-align Public

    C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.

    Cython 5 Apache-2.0 6 0 0 Updated Mar 19, 2024
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