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    20 repositories

    • giql

      Public
      SQL dialect for genomic range queries.
      Python
      •0•5•0•0•Updated Dec 19, 2025Dec 19, 2025

    • jointly-hic

      Public
      Genomics research toolkit for jointly embedding Hi-C 3D chromatin contact matrices into the same vector space
      Python
      •
      GNU General Public License v3.0
      •1•8•1•1•Updated Dec 17, 2025Dec 17, 2025

    • oxbow

      Public
      Oxbow makes genomic data ready for high-performance analytics.
      pythondata-sciencebioinformaticsrgenomicsngspandasrust-langdataframefair-data
      Rust
      •
      Apache License 2.0
      •13•146•7•1•Updated Dec 15, 2025Dec 15, 2025

    • oxbow-lite

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 13, 2025Jul 13, 2025

    • tcga-nmf

      Public
      TCGA ATAC-seq NMF notebook
      Python
      •0•1•0•0•Updated Jun 18, 2025Jun 18, 2025

    • giql-cicd

      Public
      CI/CD workflows for GIQL
      Shell
      •2•0•0•0•Updated May 1, 2025May 1, 2025

    • tcga-db

      Public
      Local database of TCGA metadata
      Python
      •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

    • datashader

      Public
      Quickly and accurately render even the largest data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •376•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • ldsc-python3

      Public
      LD Score Regression (LDSC)
      Python
      •
      GNU General Public License v3.0
      •366•2•0•3•Updated Oct 31, 2024Oct 31, 2024

    • snakemake-executor-plugin-lsf

      Public
      A Snakemake executor plugin for submitting jobs to a LSF cluster
      Python
      •
      MIT License
      •7•0•0•1•Updated Aug 7, 2024Aug 7, 2024

    • ipylangchat

      Public
      Simple Jupyter chat UI for LangChain
      Jupyter Notebook
      •
      MIT License
      •2•11•0•1•Updated Jul 3, 2024Jul 3, 2024

    • eigen-tour

      Public
      JavaScript
      •
      MIT License
      •1•1•0•1•Updated May 19, 2024May 19, 2024

    • deepC

      Public
      A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
      HTML
      •
      GNU General Public License v3.0
      •14•0•0•0•Updated Apr 12, 2024Apr 12, 2024

    • dask-ngs

      Public
      Scalable access to bioinformatics data with Dask and Oxbow
      Python
      •
      MIT License
      •3•1•1•5•Updated Mar 4, 2024Mar 4, 2024

    • 4dn-hg-jscatter-demo

      Public
      Jupyter Notebook
      •0•2•0•1•Updated Mar 1, 2024Mar 1, 2024

    • VCFormer

      Public
      Read and flatten VCF data into DataFrames
      Python
      •
      MIT License
      •0•4•0•0•Updated Aug 11, 2023Aug 11, 2023

    • jupyter_rfb

      Public
      Remote Frame Buffer for Jupyter
      Python
      •
      MIT License
      •16•0•0•0•Updated Jun 9, 2023Jun 9, 2023

    • saimin

      Public
      Rust
      •0•7•1•0•Updated Apr 28, 2023Apr 28, 2023

    • bbs741

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 13, 2022Nov 13, 2022

    • embedden

      Public
      Lego blocks for neighbor embedding and projection pipelines
      C++
      •
      MIT License
      •0•0•0•0•Updated Sep 20, 2020Sep 20, 2020