biocommons

All

21 repositories

python-package-cookiecutter
Public
A modern cookiecutter template based on https://github.com/fpgmaas/cookiecutter-uv/fork
Python
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MIT License
•152•0•0•0•Updated Sep 1, 2025Sep 1, 2025
python-package
Public template
Template for new biocommons packages, and source of configuration for periodic updates to derived packages
Makefile
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Apache License 2.0
•2•1•11•1•Updated Sep 1, 2025Sep 1, 2025
.github
Public
Organization-wide GitHub configuration
bioinformatics genomics sequencing genome-analysis variant-analysis variation
0•1•0•0•Updated Sep 1, 2025Sep 1, 2025
biocommons.github.io
Public
biocommons website
bioinformatics genomics sequencing genome-analysis variant-analysis variation
Python
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Apache License 2.0
•2•1•2•1•Updated Aug 31, 2025Aug 31, 2025
bioutils
Public
provides common tools and lookup tables used primarily by the hgvs and uta packages
bioinformatics genomics sequencing genome-analysis variant-analysis variation
Python
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Apache License 2.0
•18•22•4•2•Updated Aug 29, 2025Aug 29, 2025
anyvar
Public
[in development] Proof-of-Concept variation translation, validation, and registration service
bioinformatics genomics sequencing genome-analysis variant-analysis variation
Python
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Apache License 2.0
•5•13•39•5•Updated Aug 29, 2025Aug 29, 2025
biocommons.seqrepo
Public
non-redundant, compressed, journalled, file-based storage for biological sequences
bioinformatics genomics sequencing genome-analysis variant-analysis variation
Python
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Apache License 2.0
•36•42•28•1•Updated Aug 26, 2025Aug 26, 2025
hgvs
Public
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
bioinformatics genomics sequencing genome-analysis variant-analysis variation
Python
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Apache License 2.0
•96•273•50•5•Updated Aug 26, 2025Aug 26, 2025
hackathon
Public
Hackathon projects and planning.
bioinformatics
0•0•9•0•Updated Aug 11, 2025Aug 11, 2025
uta
Public
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
bioinformatics sequence-alignment sequences
Python
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Apache License 2.0
•24•65•22•0•Updated Mar 27, 2025Mar 27, 2025
seqrepo-rest-service
Public
OpenAPI-based REST interface to biological sequences and sequence metadata
bioinformatics genomics sequencing genome-analysis variant-analysis variation
Python
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Apache License 2.0
•5•4•3•0•Updated Mar 4, 2025Mar 4, 2025
mirrors-ncbi
Public
Makefile (of all things) to space-efficiently mirror selected NCBI resources
bioinformatics transcripts ncbi sequences biological-sequences
Makefile
•1•1•0•0•Updated Jan 7, 2025Jan 7, 2025
eutils
Public
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
bioinformatics genomics ncbi
Python
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Apache License 2.0
•28•63•5•0•Updated Jun 26, 2024Jun 26, 2024
uta-align
Public
C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.
bioinformatics sequence-alignment sequences
Cython
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Apache License 2.0
•5•6•0•0•Updated Mar 19, 2024Mar 19, 2024
hgvs-eval
Public
automated evaluation suite to assess tools that manipulate HGVS formatted variants
Python
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Apache License 2.0
•4•4•1•0•Updated Feb 13, 2024Feb 13, 2024
logos
Public
biocommons logos and logo-generation code
CSS
•0•0•0•0•Updated Feb 13, 2024Feb 13, 2024
hgvs-dataproviders-rest
Public
Python
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MIT License
•0•2•0•1•Updated Feb 13, 2024Feb 13, 2024
uta-clients
Public
Python
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MIT License
•0•0•0•3•Updated Jul 30, 2023Jul 30, 2023
dockerbase
Public
Parent images used by biocommons
Makefile
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MIT License
•0•0•0•0•Updated Sep 23, 2020Sep 23, 2020
hgvs-installation-test
Public
Verify that the supported installation method ('pip install --upgrade setuptools; pip install hgvs') works.
Python
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Apache License 2.0
•0•0•0•0•Updated Jan 30, 2020Jan 30, 2020
biocommons-python
Public
Declares/reserves "biocommons" for namespace packages only; see other repos for specific functionality
Python
•0•0•0•0•Updated Jul 5, 2017Jul 5, 2017