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    105 repositories

    • bedbase

      Public
      Aggregate, analyze, and serve genomic regions.
      genomic-intervals
      genomic-intervals
      Jupyter Notebook
      •0•4•6•1•Updated Apr 17, 2026Apr 17, 2026

    • bedboss

      Public
      Python pipeline for processing BED files for BEDbase
      geobed-filesbed-format
      geobed-filesbed-formatgenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•3•10•2•Updated Apr 17, 2026Apr 17, 2026

    • bedhost

      Public
      API and UI for BEDbase
      bioinformaticsservergenomics
      bioinformaticsservergenomicsrest-apibedfastapigenomic-intervals
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•2•13•2•Updated Apr 17, 2026Apr 17, 2026

    • gtars

      Public
      Performance-critical tools to manipulate, analyze, and process genomic interval data
      Rust
      •
      BSD 2-Clause "Simplified" License
      •4•26•36•5•Updated Apr 16, 2026Apr 16, 2026

    • hub.bulker.io

      Public
      Bulker registry
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•5•3•1•Updated Apr 16, 2026Apr 16, 2026

    • bedbase-loader

      Public
      BEDbase GEO bed file uploading
      bioinformatics-pipeline
      bioinformatics-pipeline
      Python
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • bbconf

      Public
      Configuration package for bedbase project
      config-managementpython-apigenomic-intervals
      config-managementpython-apigenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•0•2•3•Updated Apr 15, 2026Apr 15, 2026

    • refgetstore-node-demo

      Public
      Lightweight Node.js refget + seqcol API server backed by RefgetStore
      TypeScript
      •0•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • pepatac

      Public
      A modular, containerized pipeline for ATAC-seq data processing
      Python
      •
      BSD 2-Clause "Simplified" License
      •16•60•54•2•Updated Apr 13, 2026Apr 13, 2026

    • bulkers

      Public
      Rust
      •0•5•1•0•Updated Apr 12, 2026Apr 12, 2026

    • dockerfiles

      Public
      Sheffield lab dockerfiles
      Shell
      •
      BSD 2-Clause "Simplified" License
      •0•1•2•0•Updated Apr 11, 2026Apr 11, 2026

    • bedbase-ui

      Public
      a web interface for BEDbase
      TypeScript
      •0•0•1•0•Updated Apr 10, 2026Apr 10, 2026

    • markmeld

      Public
      A Python package for melding markdown content and YAML structured data
      markdownyamljinja2
      markdownyamljinja2pandoc
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•8•3•1•Updated Apr 4, 2026Apr 4, 2026

    • yacman

      Public
      YAML configuration manager
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•7•10•0•Updated Mar 25, 2026Mar 25, 2026

    • seqcol_paper_scripts

      Public
      Scripts used for analysis to write seq col paper.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • geniml

      Public
      Genomic interval machine learning
      machine-learningrepresentation-learninggenomic-intervals
      machine-learningrepresentation-learninggenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•22•10•1•Updated Mar 11, 2026Mar 11, 2026

    • bedshift

      Public archive
      Bedfile perturbation tool
      region-of-interestgenomic-regionsgenomic-intervals
      region-of-interestgenomic-regionsgenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•17•0•0•Updated Mar 6, 2026Mar 6, 2026

    • peppro

      Public
      A modular, containerized pipeline for PRO-seq data processing
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•11•0•0•Updated Mar 6, 2026Mar 6, 2026

    • pypiper

      Public
      Python toolkit for building restartable pipelines
      pythonbioinformaticspipeline
      pythonbioinformaticspipelinebioinformatics-pipelinepython-toolkit
      Python
      •
      BSD 2-Clause "Simplified" License
      •9•47•56•0•Updated Mar 6, 2026Mar 6, 2026

    • logmuse

      Public
      Small logging setup package
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•3•0•0•Updated Mar 6, 2026Mar 6, 2026

    • bulker-python

      Public
      Manager for multi-container computing environments
      dockerreproducible-researchcontainers
      dockerreproducible-researchcontainersenvironments
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •2•26•21•1•Updated Mar 6, 2026Mar 6, 2026

    • geo-schemas

      Public
      analysis of PEPhub GEO schemas
      Python
      •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • simpleCache

      Public
      Simplified R caching for reproducible big data projects
      R
      •
      Other
      •6•33•11•0•Updated Feb 28, 2026Feb 28, 2026

    • bulker-action

      Public
      0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

    • henge

      Public
      Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Feb 25, 2026Feb 25, 2026

    • mm_templates

      Public
      Jinja
      •0•3•0•0•Updated Feb 21, 2026Feb 21, 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

    • pararead

      Public
      Simplifies parallel processing of DNA sequencing reads
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•9•0•0•Updated Feb 3, 2026Feb 3, 2026

    • renin_atac

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

    • uniwig_paper_scripts

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