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    60 repositories

    • polars-bio

      Public
      Blazing-Fast Bioinformatic Operations on Python DataFrames
      bioinformaticsgenomicsarrow
      bioinformaticsgenomicsarrowpandasrust-langdataframesgenomic-rangesdatafusiongenomic-intervalspolars
      Python
      •
      Apache License 2.0
      •30•159•35•5•Updated Apr 29, 2026Apr 29, 2026

    • datafusion-bio-functions

      Public
      Apache DataFusion functions for bioinformatic operations
      Rust
      •
      Apache License 2.0
      •1•1•25•20•Updated Apr 29, 2026Apr 29, 2026

    • ds-notebooks

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •47•5•3•1•Updated Apr 28, 2026Apr 28, 2026

    • vepyr

      Public
      vepyr (/ˈvaɪpər/) — VEP Yielding Performant Results — a blazing-fast Rust reimplementation of Ensembl's Variant Effect Predictor.
      veppolars
      veppolars
      Python
      •
      Apache License 2.0
      •0•5•2•2•Updated Apr 27, 2026Apr 27, 2026

    • datafusion-bio-formats

      Public
      Apache DataFusion table providers for bioinformatic file formats
      Rust
      •
      Other
      •2•7•12•17•Updated Apr 25, 2026Apr 25, 2026

    • polars-bio-bench

      Public
      Benchmarks of various genomic ranges operations
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•2•0•Updated Apr 25, 2026Apr 25, 2026

    • vepyr-diffly

      Public
      Python
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • noodles

      Public
      Bioinformatics I/O libraries in Rust
      Rust
      •
      MIT License
      •71•0•0•1•Updated Mar 4, 2026Mar 4, 2026

    • sequila-native

      Public archive
      A set of native implementation of common bioinformatics algorithms to be used as Arrow-Datafusion or SeQuiLa (Apache Spark) extensions.
      Rust
      •
      Apache License 2.0
      •0•1•18•0•Updated Feb 16, 2026Feb 16, 2026

    • bioformats-benchmark

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 14, 2026Feb 14, 2026

    • gdl-infra

      Public
      Infrastructure for genomic open data lakehouse
      Go Template
      •0•0•0•0•Updated Feb 1, 2026Feb 1, 2026

    • edugen-notebooks

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Oct 26, 2025Oct 26, 2025

    • needletail

      Public
      Fast FASTX parsing and k-mer methods in Rust
      Rust
      •
      MIT License
      •31•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • polars-bio-workshop

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Sep 15, 2025Sep 15, 2025

    • fusion-ensemble-calling

      Public
      Python
      •0•0•0•0•Updated Sep 14, 2025Sep 14, 2025

    • datafusion-python

      Public
      Apache DataFusion Python Bindings
      Python
      •
      Apache License 2.0
      •152•0•0•0•Updated Aug 23, 2025Aug 23, 2025

    • evo2

      Public
      Genome modeling and design across all domains of life
      Jupyter Notebook
      •
      Apache License 2.0
      •487•0•0•0•Updated Mar 23, 2025Mar 23, 2025

    • biodatageeks.github.io

      Public
      TeX
      •
      MIT License
      •0•0•0•1•Updated Mar 20, 2025Mar 20, 2025

    • big-data-lab

      Public
      Self service for Data Science labs
      HCL
      •
      Apache License 2.0
      •48•0•2•1•Updated Jan 18, 2025Jan 18, 2025

    • datafusion-comet

      Public
      Apache DataFusion Comet Spark Accelerator
      Rust
      •
      Apache License 2.0
      •307•0•0•1•Updated Nov 24, 2024Nov 24, 2024

    • phenodb

      Public
      Serverless vector database for deep phenotyping
      Apache License 2.0
      •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • Llama2-HPO-Normalization

      Public
      Fine-tuning LLaMA 2 for rare disease concept normalization
      Jupyter Notebook
      •3•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • sequila

      Public
      SeQuiLa: Distributed analytics for genomics based on Apache Spark!
      HTML
      •
      Apache License 2.0
      •7•10•23•8•Updated Aug 2, 2024Aug 2, 2024

    • PhenoGPT

      Public
      Jupyter Notebook
      •
      MIT License
      •8•0•0•0•Updated May 16, 2024May 16, 2024

    • jupyter-launcher-shortcuts

      Public
      Launcher shortcuts for classic Jupyter Notebook & JupyterLab
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • PhenoTagger

      Public
      PhenoTagger
      GAP
      •
      MIT License
      •16•0•0•0•Updated Jan 24, 2024Jan 24, 2024

    • rnafusion

      Public
      RNA-seq analysis pipeline for detection gene-fusions
      Nextflow
      •
      MIT License
      •120•0•0•0•Updated Dec 1, 2023Dec 1, 2023

    • rust-bio

      Public
      This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tes…
      Rust
      •
      MIT License
      •215•1•0•0•Updated Nov 18, 2023Nov 18, 2023

    • coitrees

      Public
      A very fast interval tree data structure
      Rust
      •
      MIT License
      •10•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • iitii

      Public
      Implicit Interval Tree with Interpolation Index
      Jupyter Notebook
      •
      Apache License 2.0
      •4•0•0•0•Updated Nov 9, 2023Nov 9, 2023
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