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    101 repositories

    • pepatac

      Public
      A modular, containerized pipeline for ATAC-seq data processing
      Python
      •
      BSD 2-Clause "Simplified" License
      •16•60•53•2•Updated Feb 13, 2026Feb 13, 2026

    • pypiper

      Public
      Python toolkit for building restartable pipelines
      pythonbioinformaticspipelinebioinformatics-pipelinepython-toolkit
      Python
      •
      BSD 2-Clause "Simplified" License
      •9•45•56•2•Updated Feb 13, 2026Feb 13, 2026

    • gtars

      Public
      Performance-critical tools to manipulate, analyze, and process genomic interval data
      Rust
      •
      BSD 2-Clause "Simplified" License
      •4•23•36•0•Updated Feb 12, 2026Feb 12, 2026

    • henge

      Public
      Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•1•Updated Feb 12, 2026Feb 12, 2026

    • yacman

      Public
      YAML configuration manager
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•6•10•2•Updated Feb 11, 2026Feb 11, 2026

    • bedhost

      Public
      API and UI for BEDbase
      bioinformaticsservergenomicsrest-apibedfastapigenomic-intervals
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•2•13•2•Updated Feb 11, 2026Feb 11, 2026

    • ai-sandbox

      Public
      a basic sandbox to collect some AI resources and example projects
      Python
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • bedbase

      Public
      Aggregate, analyze, and serve genomic regions.
      genomic-intervals
      Jupyter Notebook
      •0•4•6•0•Updated Feb 9, 2026Feb 9, 2026

    • bedbase-loader

      Public
      BEDbase GEO bed file uploading
      bioinformatics-pipeline
      Python
      •0•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • bedboss

      Public
      Python pipeline for processing BED files for BEDbase
      geobed-filesbed-formatgenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•2•11•1•Updated Feb 8, 2026Feb 8, 2026

    • bbconf

      Public
      Configuration package for bedbase project
      config-managementpython-apigenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•0•2•1•Updated Feb 6, 2026Feb 6, 2026

    • astro-reveal

      Public
      A template for combining Astro and Reveal.js to build and deploy beautiful presentation websites.
      Astro
      •0•0•0•0•Updated Feb 6, 2026Feb 6, 2026

    • bulker

      Public
      Manager for multi-container computing environments
      dockerreproducible-researchcontainersenvironments
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •2•25•21•2•Updated Feb 6, 2026Feb 6, 2026

    • peppro

      Public
      A modular, containerized pipeline for PRO-seq data processing
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•11•14•1•Updated Feb 4, 2026Feb 4, 2026

    • pararead

      Public
      Simplifies parallel processing of DNA sequencing reads
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•10•0•0•Updated Feb 3, 2026Feb 3, 2026

    • renin_atac

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • geniml

      Public
      Genomic interval machine learning
      machine-learningrepresentation-learninggenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•21•10•0•Updated Jan 14, 2026Jan 14, 2026

    • markmeld

      Public
      A Python package for melding markdown content and YAML structured data
      markdownyamljinja2pandoc
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•7•3•1•Updated Dec 18, 2025Dec 18, 2025

    • uniwig_paper_scripts

      Public
      Research applications using uniwig
      Python
      •0•0•0•0•Updated Nov 8, 2025Nov 8, 2025

    • seqcol_paper_scripts

      Public
      Scripts used for analysis to write seq col paper.
      Python
      •0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

    • sciquill

      Public
      Author academic documents in markdown
      markdownacademic-publishingcv-template
      TeX
      •5•12•4•0•Updated Oct 17, 2025Oct 17, 2025

    • mm_templates

      Public
      Jinja
      •0•3•0•0•Updated Oct 6, 2025Oct 6, 2025

    • schema.databio.org

      Public
      Repository of JSON-schemas
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •1•2•1•2•Updated Oct 2, 2025Oct 2, 2025

    • bedshift

      Public
      Bedfile perturbation tool
      region-of-interestgenomic-regionsgenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•17•5•0•Updated Sep 29, 2025Sep 29, 2025

    • mouse_sciATAC_atlas

      Public
      Python
      •8•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • hub.bulker.io

      Public
      Bulker registry
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•5•3•0•Updated Apr 29, 2025Apr 29, 2025

    • GenomicDistributions

      Public
      Calculate and plot distributions of genomic ranges
      R
      •
      Other
      •10•27•9•1•Updated Apr 23, 2025Apr 23, 2025

    • gtokenizers-bench

      Public
      Benchmark various implementations of genomic overlap methods (tokenizers) in a controlled environment.
      Rust
      •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • uniwig

      Public
      C
      •0•1•5•0•Updated Feb 10, 2025Feb 10, 2025

    • COCOA

      Public
      Annotating epigenetic variation among samples with region sets in R
      pcadna-methylation
      R
      •
      Other
      •0•11•2•1•Updated Jan 18, 2025Jan 18, 2025