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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. `pip install hgvs`

    Python 248 94

  2. uta uta Public

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

    Python 62 26

  3. bioutils bioutils Public

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

    Python 21 18

  4. biocommons.seqrepo biocommons.seqrepo Public

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

    Python 40 35

  5. eutils eutils Public

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

    Python 58 25

  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
  • anyvar Public

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

    biocommons/anyvar’s past year of commit activity
    Python 12 Apache-2.0 6 6 2 Updated Dec 11, 2024
  • hgvs Public

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

    biocommons/hgvs’s past year of commit activity
    Python 248 Apache-2.0 94 46 6 Updated Dec 11, 2024
  • biocommons.seqrepo Public

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

    biocommons/biocommons.seqrepo’s past year of commit activity
    Python 40 Apache-2.0 35 22 1 Updated Nov 25, 2024
  • 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 62 Apache-2.0 26 22 0 Updated Nov 18, 2024
  • 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 21 Apache-2.0 18 2 0 Updated Nov 4, 2024
  • biocommons.example Public template

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

    biocommons/biocommons.example’s past year of commit activity
    Makefile 1 Apache-2.0 2 4 0 Updated Sep 23, 2024
  • seqrepo-rest-service Public

    OpenAPI-based REST interface to biological sequences and sequence metadata

    biocommons/seqrepo-rest-service’s past year of commit activity
    Python 4 Apache-2.0 6 2 1 Updated Sep 1, 2024
  • biocommons.github.io Public

    biocommons website

    biocommons/biocommons.github.io’s past year of commit activity
    Python 1 Apache-2.0 2 1 0 Updated Sep 1, 2024
  • eutils Public

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

    biocommons/eutils’s past year of commit activity
    Python 58 Apache-2.0 25 4 0 Updated Jun 26, 2024
  • .github Public

    Organization-wide GitHub configuration

    biocommons/.github’s past year of commit activity
    1 0 0 0 Updated Apr 22, 2024
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