Repositories list

• geofetch

  Public

  pepkit/geofetch’s past year of commit activity
  Builds a PEP from SRA or GEO accessions

  metadatageodownload-manager+ 2

  metadatageodownload-managersrasra-data

  Python

  •

  BSD 2-Clause "Simplified" License

  •66 forks•5555 stars•77 issues•00 pull requests•Updated Apr 12, 2026Apr 12, 2026

• pipestat

  Public
  Pipeline results reporting package

  pythoninterfacereporting+ 4

  pythoninterfacereportingpostgresqlpipelinesresultsreproducibility

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•44 stars•1010 issues•00 pull requests•Updated Apr 11, 2026Apr 11, 2026

• looper

  Public
  Modular job submitter for arbitrary pipelines or commands.

  bioinformaticsngsbioinformatics-pipeline+ 1

  bioinformaticsngsbioinformatics-pipelinepipeline-submission-engine

  Python

  •

  BSD 2-Clause "Simplified" License

  •77 forks•2626 stars•1212 issues•00 pull requests•Updated Apr 11, 2026Apr 11, 2026

• pephub

  Public
  A web API and database for biological sample metadata

  bioinformaticsdata-sharingmetadata-management+ 1

  bioinformaticsdata-sharingmetadata-managementsample-metadata

  TypeScript

  •

  BSD 2-Clause "Simplified" License

  •22 forks•2222 stars•6767 issues•11 pull request•Updated Apr 10, 2026Apr 10, 2026

• pepdbagent

  Public

  pepkit/pepdbagent’s past year of commit activity
  Database for storing sample metadata

  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•22 stars•88 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• pepembed

  Public
  Indexer of pephub database

  Python

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

• geopephub

  Public
  Automatic uploader of GEO metadata to PEPhub.

  Python

  •

  BSD 2-Clause "Simplified" License

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

• ubiquerg

  Public
  Tools for work (erg) everywhere (ubique)

  utility-library

  utility-library

  Python

  •

  BSD 2-Clause "Simplified" License

  •33 forks•11 star•00 issues•00 pull requests•Updated Apr 2, 2026Apr 2, 2026

• peppy

  Public
  Project metadata manager for PEPs in Python

  metadatabioinformaticsngs+ 2

  metadatabioinformaticsngspipeline-submission-enginemetadata-management

  Python

  •

  BSD 2-Clause "Simplified" License

  •1313 forks•4040 stars•3333 issues•11 pull request•Updated Apr 1, 2026Apr 1, 2026

• pepspec

  Public
  Documentation for PEP specification and all PEPkit software

  HTML

  •44 forks•1010 stars•44 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• attmap

  Public
  Key-value mapping that supports nested attribute-style access

  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•44 stars•11 issue•11 pull request•Updated Mar 25, 2026Mar 25, 2026

• divvy

  Public archive
  Standardized computing resource configuration

  configuration-managementhigh-performance-computing

  configuration-managementhigh-performance-computing

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•44 stars•77 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• pephubclient

  Public
  A tool to provide Python and CLI interface and Python API for PEPhub.

  pythonbioinformaticsproject+ 1

  pythonbioinformaticsprojectcommand-line-tool

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•33 stars•1010 issues•00 pull requests•Updated Mar 18, 2026Mar 18, 2026

• pepr

  Public
  Project metadata manager for PEPs in R

  metadatabioinformatics

  metadatabioinformatics

  R

  •

  Other

  •11 fork•33 stars•22 issues•00 pull requests•Updated Feb 28, 2026Feb 28, 2026

• eido

  Public
  Validator for PEP objects

  metadatavalidationpep+ 2

  metadatavalidationpepconversionjsonschema

  Python

  •

  BSD 2-Clause "Simplified" License

  •55 forks•55 stars•55 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• pipestat_reader

  Public archive
  web API generator for pipeline results

  graphqldatabaseapi-documentation+ 2

  graphqldatabaseapi-documentationpipeline-frameworkresults-viewer

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2025Sep 22, 2025

• veracitools

  Public archive
  Testing utilities - DEPRECATED

  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•11 star•00 issues•00 pull requests•Updated Sep 22, 2025Sep 22, 2025

• hello_looper

  Public
  A Hello World! example repository for looper

  Python

  •55 forks•00 stars•00 issues•00 pull requests•Updated Oct 2, 2024Oct 2, 2024

• pep-pipelines

  Public
  Examples of how to use PEP to run pipelines with different workflow systems

  Python

  •00 forks•11 star•11 issue•00 pull requests•Updated Dec 22, 2023Dec 22, 2023

• pep-snakemake

  Public archive
  Example simple and bioinformatic pipelines using PEPs and snakemake.

  snakemakepipelinepep

  snakemakepipelinepep

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 1, 2023Dec 1, 2023

• pep-cwl

  Public archive
  Common Workflow Language

  •00 forks•11 star•00 issues•11 pull request•Updated Dec 1, 2023Dec 1, 2023

• pep-nextflow

  Public archive
  00 forks•00 stars•00 issues•11 pull request•Updated Dec 1, 2023Dec 1, 2023

• example_peps

  Public
  Some simple examples of PEP-compatible projects

  Jupyter Notebook

  •22 forks•00 stars•22 issues•00 pull requests•Updated Nov 16, 2023Nov 16, 2023

• BiocProject

  Public
  BiocProject provides a PEP-compatible R package for autoloading biological data

  R

  •

  Other

  •11 fork•33 stars•33 issues•11 pull request•Updated Jul 18, 2023Jul 18, 2023

• pephub.databio.org

  Public archive
  Data stores for pephub PEPs

  Shell

  •00 forks•00 stars•22 issues•00 pull requests•Updated Jun 8, 2023Jun 8, 2023

• example-pephub-spa

  Public
  TypeScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 8, 2023Mar 8, 2023

• example-pephub-cli

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2023Mar 7, 2023

• pephub-ui

  Public
  TypeScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 22, 2023Feb 22, 2023

• pepingester

  Public
  Python

  •00 forks•00 stars•11 issue•00 pull requests•Updated Sep 3, 2022Sep 3, 2022

• divcfg

  Public
  DIvvy computing configuration files.

  Shell

  •

  BSD 2-Clause "Simplified" License

  •33 forks•44 stars•22 issues•00 pull requests•Updated Aug 29, 2022Aug 29, 2022