biocommons

a collection of open source bioinformatics tools

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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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hgvshgvsPublic
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Python 260 95
utautaPublic
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Python 63 25
bioutilsbioutilsPublic
provides common tools and lookup tables used primarily by the hgvs and uta packages
Python 22 18
biocommons.seqrepobiocommons.seqrepoPublic
non-redundant, compressed, journalled, file-based storage for biological sequences
Python 40 34
eutilseutilsPublic
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
Python 59 27
seqrepo-rest-serviceseqrepo-rest-servicePublic
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
biocommons/anyvar’s past year of commit activity
Python 13Apache-2.0 5 8 2 UpdatedMar 6, 2025
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 260Apache-2.0 95 48 4 UpdatedMar 5, 2025
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 22Apache-2.0 18 2 1 UpdatedMar 5, 2025
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 4Apache-2.0 5 2 0 UpdatedMar 4, 2025
biocommons.seqrepo Public
non-redundant, compressed, journalled, file-based storage for biological sequences
biocommons/biocommons.seqrepo’s past year of commit activity
Python 40Apache-2.0 34 26 0 UpdatedMar 4, 2025
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 63Apache-2.0 25 21 0 UpdatedFeb 3, 2025
mirrors-ncbi Public
Makefile (of all things) to space-efficiently mirror selected NCBI resources
biocommons/mirrors-ncbi’s past year of commit activity
Makefile 1 1 0 0 UpdatedJan 7, 2025
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 1Apache-2.0 2 4 0 UpdatedSep 23, 2024
biocommons.github.io Public
biocommons website
biocommons/biocommons.github.io’s past year of commit activity
Python 1Apache-2.0 2 2 0 UpdatedSep 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 59Apache-2.0 27 5 0 UpdatedJun 26, 2024