Repositories list

• peppy

  Public
  Project metadata manager for PEPs in Python

  metadatabioinformaticsngs+ 2pipeline-submission-enginemetadata-management

  Python

  •

  BSD 2-Clause "Simplified" License

  •13•38•34•2•Updated Dec 22, 2025Dec 22, 2025

• pepspec

  Public
  Documentation for PEP specification and all PEPkit software

  HTML

  •4•10•4•1•Updated Dec 22, 2025Dec 22, 2025

• geopephub

  Public
  Automatic uploader of GEO metadata to PEPhub.

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•3•0•Updated Dec 22, 2025Dec 22, 2025

• pephub

  Public
  A web API and database for biological sample metadata

  bioinformaticsdata-sharingmetadata-management+ 1sample-metadata

  TypeScript

  •

  BSD 2-Clause "Simplified" License

  •2•20•67•0•Updated Dec 16, 2025Dec 16, 2025

• pepembed

  Public
  Indexer of pephub database

  Python

  •0•1•1•0•Updated Dec 16, 2025Dec 16, 2025

• geofetch

  Public
  Builds a PEP from SRA or GEO accessions

  metadatageodownload-manager+ 2srasra-data

  Python

  •

  BSD 2-Clause "Simplified" License

  •6•54•7•1•Updated Dec 1, 2025Dec 1, 2025

• ubiquerg

  Public
  Tools for work (erg) everywhere (ubique)

  utility-library

  Python

  •

  BSD 2-Clause "Simplified" License

  •3•1•0•0•Updated Dec 1, 2025Dec 1, 2025

• pipestat

  Public
  Pipeline results reporting package

  pythoninterfacereporting+ 4postgresqlpipelinesresultsreproducibility

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•4•9•0•Updated Nov 6, 2025Nov 6, 2025

• looper

  Public
  Modular job submitter for arbitrary pipelines or commands.

  bioinformaticsngsbioinformatics-pipeline+ 1pipeline-submission-engine

  Python

  •

  BSD 2-Clause "Simplified" License

  •7•24•12•1•Updated Nov 6, 2025Nov 6, 2025

• eido

  Public
  Validator for PEP objects

  metadatavalidationpep+ 2conversionjsonschema

  Python

  •

  BSD 2-Clause "Simplified" License

  •5•5•5•0•Updated Oct 7, 2025Oct 7, 2025

• pipestat_reader

  Public archive
  web API generator for pipeline results

  graphqldatabaseapi-documentation+ 2pipeline-frameworkresults-viewer

  Python

  •0•0•0•0•Updated Sep 22, 2025Sep 22, 2025

• divvy

  Public archive
  Standardized computing resource configuration

  configuration-managementhigh-performance-computing

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•4•7•0•Updated Sep 22, 2025Sep 22, 2025

• veracitools

  Public archive
  Testing utilities - DEPRECATED

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•1•0•0•Updated Sep 22, 2025Sep 22, 2025

• pepdbagent

  Public
  Database for storing sample metadata

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•2•8•0•Updated May 19, 2025May 19, 2025

• pephubclient

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

  pythonbioinformaticsproject+ 1command-line-tool

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•3•10•1•Updated Apr 11, 2025Apr 11, 2025

• hello_looper

  Public
  A Hello World! example repository for looper

  Python

  •5•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• pepr

  Public
  Project metadata manager for PEPs in R

  metadatabioinformatics

  R

  •

  Other

  •1•3•3•1•Updated Aug 5, 2024Aug 5, 2024

• attmap

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

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•4•10•1•Updated May 10, 2024May 10, 2024

• pep-pipelines

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

  Python

  •0•1•1•0•Updated Dec 22, 2023Dec 22, 2023

• pep-snakemake

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

  snakemakepipelinepep

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Dec 1, 2023Dec 1, 2023

• pep-cwl

  Public archive
  Common Workflow Language

  •0•1•0•1•Updated Dec 1, 2023Dec 1, 2023

• pep-nextflow

  Public archive
  0•0•0•1•Updated Dec 1, 2023Dec 1, 2023

• example_peps

  Public
  Some simple examples of PEP-compatible projects

  Jupyter Notebook

  •2•0•2•0•Updated Nov 16, 2023Nov 16, 2023

• BiocProject

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

  R

  •

  Other

  •1•3•3•1•Updated Jul 18, 2023Jul 18, 2023

• pephub.databio.org

  Public archive
  Data stores for pephub PEPs

  Shell

  •0•0•2•0•Updated Jun 8, 2023Jun 8, 2023

• example-pephub-spa

  Public
  TypeScript

  •0•0•0•0•Updated Mar 8, 2023Mar 8, 2023

• example-pephub-cli

  Public
  Python

  •0•0•0•0•Updated Mar 7, 2023Mar 7, 2023

• pephub-ui

  Public
  TypeScript

  •0•0•0•0•Updated Feb 22, 2023Feb 22, 2023

• pepingester

  Public
  Python

  •0•0•1•0•Updated Sep 3, 2022Sep 3, 2022

• divcfg

  Public
  DIvvy computing configuration files.

  Shell

  •

  BSD 2-Clause "Simplified" License

  •3•4•2•0•Updated Aug 29, 2022Aug 29, 2022