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@genomoncology GenomOncology, LLC

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    25 repositories

    • biomcp

      Public
      BioMCP: Biomedical Model Context Protocol
      bioinformaticsaigenomicsmcppubmedpubmed-centralmedicalclinical-trialsllmmodel-context-protocol
      Python
      •
      MIT License
      •10•95•3•1•Updated Apr 30, 2025Apr 30, 2025

    • biomcp-examples

      Public
      Example chats from running BioMCP for demonstrations
      MIT License
      •0•5•0•0•Updated Apr 18, 2025Apr 18, 2025

    • biocommons.seqrepo

      Public
      non-redundant, compressed, journalled, file-based storage for biological sequences
      Python
      •
      Apache License 2.0
      •35•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • hgvs

      Public
      Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
      Python
      •
      Apache License 2.0
      •95•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • pysam

      Public
      Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
      Cython
      •
      MIT License
      •283•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • rigor

      Public
      HTTP-based DSL for for validating RESTful APIs
      pythonpython3aiohttprequestsasyncioapi-testing-framework
      Python
      •
      MIT License
      •6•70•1•3•Updated Aug 13, 2024Aug 13, 2024

    • swagger-codegen

      Public
      swagger-codegen contains a template-driven engine to generate documentation, API clients and server stubs in different languages by parsing your OpenAPI / Swagger definition.
      HTML
      •
      Other
      •6k•0•0•1•Updated Aug 9, 2024Aug 9, 2024

    • hgvs-rs

      Public
      A port of biocommons/hgvs to the Rust programming language
      Rust
      •
      Apache License 2.0
      •5•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • FuzzTypes

      Public archive
      Pydantic extension for annotating autocorrecting fields.
      data-cleaningfuzzy-string-matchingnamed-entity-linkingpydantic
      Python
      •
      MIT License
      •4•220•0•0•Updated Jun 20, 2024Jun 20, 2024

    • django-multiselectfield

      Public
      A Multiple Choice model field
      Python
      •
      GNU Lesser General Public License v3.0
      •210•0•0•0•Updated Apr 9, 2024Apr 9, 2024

    • uta

      Public
      Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
      Python
      •
      Apache License 2.0
      •25•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • AIONER-docker

      Public
      AIONER
      Python
      •
      MIT License
      •15•0•0•0•Updated Mar 11, 2024Mar 11, 2024

    • related

      Public
      Nested Object Models in Python with dictionary, YAML, and JSON transformation support
      jsonobject-relational-mapperpythonyaml
      Python
      •
      MIT License
      •15•203•15•7•Updated Dec 27, 2022Dec 27, 2022

    • specd

      Public
      Swagger v2 Specification Directories
      Python
      •
      MIT License
      •0•3•1•1•Updated Dec 9, 2022Dec 9, 2022

    • parsley-cython

      Public
      Parsley (v1.3) compiled using Cython to improve parse performance
      Python
      •
      Other
      •50•0•0•0•Updated Sep 21, 2022Sep 21, 2022

    • django-suit

      Public
      Modern theme for Django admin interface
      SCSS
      •
      Other
      •707•0•0•0•Updated Jun 9, 2022Jun 9, 2022

    • hopeIQ

      Public
      Python
      •0•1•0•0•Updated Apr 13, 2021Apr 13, 2021

    • django-rest-swagger

      Public
      Swagger Documentation Generator for Django REST Framework: deprecated
      Python
      •
      BSD 2-Clause "Simplified" License
      •606•0•0•0•Updated Apr 8, 2021Apr 8, 2021

    • celery

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Dec 1, 2020Dec 1, 2020

    • using-cyvcf2

      Public
      Repository for Blog Article on Parsing with cyvcf2. Article ==>
      bioinformaticsvcftoolscyvcf2
      Python
      •1•7•0•0•Updated May 16, 2020May 16, 2020

    • dockprom

      Public
      Docker hosts and containers monitoring with Prometheus, Grafana, cAdvisor, NodeExporter and AlertManager
      Shell
      •
      MIT License
      •1.7k•0•0•0•Updated Jun 20, 2019Jun 20, 2019

    • pysolr

      Public
      Pysolr — Python Solr client
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •340•0•0•0•Updated Jun 4, 2019Jun 4, 2019

    • django-prometheus

      Public
      Export Django monitoring metrics for Prometheus.io
      Python
      •
      Apache License 2.0
      •249•0•0•0•Updated Feb 22, 2019Feb 22, 2019

    • pdf-annotate.js

      Public
      Annotation layer for pdf.js (no longer maintained)
      JavaScript
      •
      MIT License
      •273•0•0•0•Updated Dec 21, 2018Dec 21, 2018

    • nexus-repository-import-scripts

      Public
      A few scripts for importing artifacts into Nexus Repository
      Shell
      •
      Apache License 2.0
      •104•0•0•0•Updated Aug 1, 2017Aug 1, 2017
    0