Repositories list

• gtars

  Public
  Performance-critical tools to manipulate, analyze, and process genomic interval data

  Rust

  •

  BSD 2-Clause "Simplified" License

  •4•24•36•5•Updated Mar 2, 2026Mar 2, 2026

• bedbase-loader

  Public
  BEDbase GEO bed file uploading

  bioinformatics-pipeline

  Python

  •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• simpleCache

  Public
  Simplified R caching for reproducible big data projects

  R

  •

  Other

  •6•33•11•0•Updated Feb 28, 2026Feb 28, 2026

• pypiper

  Public
  Python toolkit for building restartable pipelines

  pythonbioinformaticspipeline+ 2bioinformatics-pipelinepython-toolkit

  Python

  •

  BSD 2-Clause "Simplified" License

  •9•46•56•1•Updated Feb 28, 2026Feb 28, 2026

• bulkers

  Public
  Rust

  •0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

• bedboss

  Public
  Python pipeline for processing BED files for BEDbase

  geobed-filesbed-format+ 1genomic-intervals

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•2•10•1•Updated Feb 27, 2026Feb 27, 2026

• bbconf

  Public
  Configuration package for bedbase project

  config-managementpython-apigenomic-intervals

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•0•1•2•Updated Feb 27, 2026Feb 27, 2026

• bedbase-ui

  Public
  a modular web interface for BEDbase

  TypeScript

  •0•0•1•0•Updated Feb 27, 2026Feb 27, 2026

• bedhost

  Public
  API and UI for BEDbase

  bioinformaticsservergenomics+ 4rest-apibedfastapigenomic-intervals

  TypeScript

  •

  BSD 2-Clause "Simplified" License

  •1•2•11•1•Updated Feb 27, 2026Feb 27, 2026

• bulker-python

  Public
  Manager for multi-container computing environments

  dockerreproducible-researchcontainers+ 1environments

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •2•26•21•1•Updated Feb 27, 2026Feb 27, 2026

• hub.bulker.io

  Public
  Bulker registry

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•5•3•1•Updated Feb 27, 2026Feb 27, 2026

• bulker-action

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

• peppro

  Public
  A modular, containerized pipeline for PRO-seq data processing

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•11•0•1•Updated Feb 25, 2026Feb 25, 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

• bedbase

  Public
  Aggregate, analyze, and serve genomic regions.

  genomic-intervals

  Jupyter Notebook

  •0•4•6•0•Updated Feb 24, 2026Feb 24, 2026

• geo-schemas

  Public
  analysis of PEPhub GEO schemas

  Python

  •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

• yacman

  Public
  YAML configuration manager

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•6•10•1•Updated Feb 23, 2026Feb 23, 2026

• mm_templates

  Public
  Jinja

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

• pepatac

  Public
  A modular, containerized pipeline for ATAC-seq data processing

  Python

  •

  BSD 2-Clause "Simplified" License

  •16•60•53•2•Updated Feb 18, 2026Feb 18, 2026

• markmeld

  Public
  A Python package for melding markdown content and YAML structured data

  markdownyamljinja2+ 1pandoc

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•7•3•1•Updated Feb 17, 2026Feb 17, 2026

• ai-sandbox

  Public
  a basic sandbox to collect some AI resources and example projects

  Python

  •0•1•0•0•Updated Feb 15, 2026Feb 15, 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

• 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

• 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

• 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