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    49 repositories

    • biodatageeks.github.io

      Public
      TeX
      •
      MIT License
      •0•0•0•1•Updated Feb 21, 2025Feb 21, 2025

    • polars-bio

      Public
      Blazing-Fast Bioinformatic Operations on Python DataFrames
      bioinformaticsgenomicsarrowpandasrust-langdataframesgenomic-rangesdatafusiongenomic-intervalspolars
      Python
      •
      Apache License 2.0
      •1•7•18•4•Updated Feb 20, 2025Feb 20, 2025

    • datafusion-bio-formats

      Public
      Apache License 2.0
      •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

    • sequila-native

      Public
      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•0•18•0•Updated Feb 12, 2025Feb 12, 2025

    • polars-bio-bench

      Public
      Benchmarks of various genomic ranges operations
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•1•1•Updated Feb 12, 2025Feb 12, 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

    • ds-notebooks

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •46•5•3•1•Updated Jan 18, 2025Jan 18, 2025

    • datafusion-comet

      Public
      Apache DataFusion Comet Spark Accelerator
      Rust
      •
      Apache License 2.0
      •182•0•0•1•Updated Nov 24, 2024Nov 24, 2024

    • edugen-notebooks

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Oct 27, 2024Oct 27, 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
      •6•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
      •11•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
      •104•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 tested via continuous integration.
      Rust
      •
      MIT License
      •204•0•0•0•Updated Nov 18, 2023Nov 18, 2023

    • coitrees

      Public
      A very fast interval tree data structure
      Rust
      •
      MIT License
      •8•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

    • rich-bench

      Public
      A little benchmarking tool for Python
      Python
      •
      MIT License
      •6•0•0•0•Updated Oct 15, 2023Oct 15, 2023

    • PhenoRerank

      Public
      Python
      •2•0•0•0•Updated Aug 24, 2023Aug 24, 2023

    • ds-images

      Public
      Shell
      •
      Apache License 2.0
      •0•0•15•4•Updated May 25, 2023May 25, 2023

    • sparkseq

      Public
      Scala
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 5, 2023Mar 5, 2023

    • popgen

      Public
      Scala
      •0•0•0•0•Updated Mar 5, 2023Mar 5, 2023

    • variantsdwh

      Public
      Scala
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 5, 2023Mar 5, 2023

    • disq

      Public
      A library for manipulating bioinformatics sequencing formats in Apache Spark
      Java
      •
      MIT License
      •11•1•0•0•Updated Jan 29, 2023Jan 29, 2023

    • cannoli

      Public
      Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •17•0•0•0•Updated Jan 29, 2023Jan 29, 2023

    • phenotype_embedding

      Public
      Python
      •2•0•0•0•Updated Jan 17, 2023Jan 17, 2023

    • sequila-cloud-recipes

      Public
      SeQuiLa recipes, examples and other cloud-related content
      HCL
      •
      Apache License 2.0
      •1•3•0•0•Updated Nov 15, 2022Nov 15, 2022

    • pysequila

      Public
      Python wrapper for SeQuiLa: Distributed analytics for genomics based on Apache Spark!
      HTML
      •
      Apache License 2.0
      •1•2•3•3•Updated Nov 4, 2022Nov 4, 2022