Pinned Repositories
anyvar
[in development] Proof-of-Concept variation translation, validation, and registration service
biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
bioutils
provides common tools and lookup tables used primarily by the hgvs and uta packages
eutils
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
hgvs-dataproviders-rest
hgvs-eval
automated evaluation suite to assess tools that manipulate HGVS formatted variants
seqrepo-rest-service
OpenAPI-based REST interface to biological sequences and sequence metadata
uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
uta-align
C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.
biocommons's Repositories
biocommons/hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
biocommons/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
biocommons/eutils
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
biocommons/biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
biocommons/bioutils
provides common tools and lookup tables used primarily by the hgvs and uta packages
biocommons/anyvar
[in development] Proof-of-Concept variation translation, validation, and registration service
biocommons/uta-align
C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.
biocommons/hgvs-eval
automated evaluation suite to assess tools that manipulate HGVS formatted variants
biocommons/seqrepo-rest-service
OpenAPI-based REST interface to biological sequences and sequence metadata
biocommons/hgvs-dataproviders-rest
biocommons/.github
Organization-wide GitHub configuration
biocommons/biocommons.example
Template for new biocommons packages, and source of configuration for periodic updates to derived packages
biocommons/biocommons.github.io
biocommons website
biocommons/hackathon-2023
Hackathon 2023 projects and planning.
biocommons/mirrors-ncbi
Makefile (of all things) to space-efficiently mirror selected NCBI resources
biocommons/biocommons-python
Declares/reserves "biocommons" for namespace packages only; see other repos for specific functionality
biocommons/dockerbase
Parent images used by biocommons
biocommons/hgvs-installation-test
Verify that the supported installation method ('pip install --upgrade setuptools; pip install hgvs') works.
biocommons/logos
biocommons logos and logo-generation code
biocommons/uta-clients