Repositories list

• gtars

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

  Rust

  •

  BSD 2-Clause "Simplified" License

  •44 forks•2626 stars•3636 issues•44 pull requests•Updated Apr 11, 2026Apr 11, 2026

• bedbase-ui

  Public
  a web interface for BEDbase

  TypeScript

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• bedhost

  Public
  API and UI for BEDbase

  bioinformaticsservergenomics+ 4

  bioinformaticsservergenomicsrest-apibedfastapigenomic-intervals

  TypeScript

  •

  BSD 2-Clause "Simplified" License

  •11 fork•22 stars•1111 issues•22 pull requests•Updated Apr 10, 2026Apr 10, 2026

• bedboss

  Public
  Python pipeline for processing BED files for BEDbase

  geobed-filesbed-format+ 1

  geobed-filesbed-formatgenomic-intervals

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•33 stars•1010 issues•22 pull requests•Updated Apr 9, 2026Apr 9, 2026

• hub.bulker.io

  Public
  Bulker registry

  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•55 stars•33 issues•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• bbconf

  Public

  databio/bbconf’s past year of commit activity
  Configuration package for bedbase project

  config-managementpython-apigenomic-intervals

  config-managementpython-apigenomic-intervals

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•00 stars•11 issue•33 pull requests•Updated Apr 7, 2026Apr 7, 2026

• bedbase-loader

  Public
  BEDbase GEO bed file uploading

  bioinformatics-pipeline

  bioinformatics-pipeline

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 6, 2026Apr 6, 2026

• dockerfiles

  Public
  Sheffield lab dockerfiles

  Shell

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•22 issues•00 pull requests•Updated Apr 6, 2026Apr 6, 2026

• markmeld

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

  markdownyamljinja2+ 1

  markdownyamljinja2pandoc

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•77 stars•33 issues•11 pull request•Updated Apr 4, 2026Apr 4, 2026

• pepatac

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

  Python

  •

  BSD 2-Clause "Simplified" License

  •1616 forks•6060 stars•5454 issues•11 pull request•Updated Mar 26, 2026Mar 26, 2026

• bulkers

  Public
  Rust

  •00 forks•44 stars•11 issue•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• yacman

  Public
  YAML configuration manager

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•77 stars•1010 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•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

  •33 forks•2222 stars•1010 issues•11 pull request•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

  •33 forks•1717 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• peppro

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

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•1111 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• pypiper

  Public
  Python toolkit for building restartable pipelines

  pythonbioinformaticspipeline+ 2

  pythonbioinformaticspipelinebioinformatics-pipelinepython-toolkit

  Python

  •

  BSD 2-Clause "Simplified" License

  •99 forks•4747 stars•5656 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• logmuse

  Public
  Small logging setup package

  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•33 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• bulker-python

  Public
  Manager for multi-container computing environments

  dockerreproducible-researchcontainers+ 1

  dockerreproducible-researchcontainersenvironments

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •22 forks•2626 stars•2121 issues•11 pull request•Updated Mar 6, 2026Mar 6, 2026

• geo-schemas

  Public
  analysis of PEPhub GEO schemas

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• simpleCache

  Public
  Simplified R caching for reproducible big data projects

  R

  •

  Other

  •66 forks•3333 stars•1111 issues•00 pull requests•Updated Feb 28, 2026Feb 28, 2026

• bulker-action

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 26, 2026Feb 26, 2026

• henge

  Public
  Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 25, 2026Feb 25, 2026

• bedbase

  Public
  Aggregate, analyze, and serve genomic regions.

  genomic-intervals

  genomic-intervals

  Jupyter Notebook

  •00 forks•44 stars•66 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• mm_templates

  Public
  Jinja

  •00 forks•33 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 6, 2026Feb 6, 2026

• pararead

  Public
  Simplifies parallel processing of DNA sequencing reads

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•99 stars•00 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• renin_atac

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 28, 2026Jan 28, 2026

• uniwig_paper_scripts

  Public
  Research applications using uniwig

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 8, 2025Nov 8, 2025

• sciquill

  Public
  Author academic documents in markdown

  markdownacademic-publishingcv-template

  markdownacademic-publishingcv-template

  TeX

  •55 forks•1212 stars•44 issues•00 pull requests•Updated Oct 17, 2025Oct 17, 2025