Repositories list

• COPO-production

  Public
  COPO is a Django-based platform that serves as a metadata broker to describe research data per FAIR principles. It supports community-recognised metadata standa…

  researchgenomicsomics+ 3

  researchgenomicsomicsbiodiversitylife-sciencesmetadata-broker

  JavaScript

  •

  MIT License

  •2•5•0•3•Updated Mar 27, 2026Mar 27, 2026

• eista

  Public
  A single-cell spatial transcriptomics pipeline aimed at covering all analysis stages from quantification and clustering to tertiary analyses.

  Python

  •

  MIT License

  •0•2•0•0•Updated Mar 24, 2026Mar 24, 2026

• eisca

  Public
  A single-cell RNA-seq pipeline aimed at covering all analysis stages from quantification and clustering to tertiary analyses.

  Python

  •

  MIT License

  •1•3•2•0•Updated Mar 24, 2026Mar 24, 2026

• grassroots_services_django_web

  Public
  JavaScript

  •1•0•0•10•Updated Mar 23, 2026Mar 23, 2026

• grassroots-service-blast

  Public
  The BLAST services for the Grassroots infrastructure

  C++

  •

  Apache License 2.0

  •0•2•0•0•Updated Mar 23, 2026Mar 23, 2026

• grassroots-core

  Public
  The core libraries of the Grassroots infratructure

  C

  •

  Apache License 2.0

  •0•1•0•0•Updated Mar 23, 2026Mar 23, 2026

• COPO-documentation

  Public
  COPO documentation was created using the Sphinx reStructuredText (reST) markup language which is hosted on readthedocs.io. The documentation uses Sphinx.

  metadatasphinxreadthedocs+ 4

  metadatasphinxreadthedocssphinx-documentationcopocopo-projectcopo-docs

  Python

  •

  Apache License 2.0

  •0•2•0•2•Updated Mar 18, 2026Mar 18, 2026

• FlowFI

  Public
  FlowFI is a python-based package for selecting important features for gating of flow cytometry events and analysis of these features.

  Python

  •1•0•0•0•Updated Mar 15, 2026Mar 15, 2026

• grassroots-server-apache-httpd

  Public
  The Apache httpd server module for the Grassroots infrastructure

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

• rfparser

  Public
  Parse ResearchFish publications to update CKAN

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

• earlham_cellxgene

  Public
  reusable dockerised instance of cellxgene with custom landing page to select between single cell datasets

  Python

  •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

• MARTi

  Public
  Metagenomic Analysis in Real Time

  Java

  •

  MIT License

  •3•0•0•0•Updated Mar 1, 2026Mar 1, 2026

• grassroots-service-field-trial

  Public
  A Grassroots service for storing the data for field trials

  C

  •

  Apache License 2.0

  •0•2•0•0•Updated Feb 24, 2026Feb 24, 2026

• grassroots-lucene

  Public
  Lucene engine customised for Grassroots data

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• grassroots-client-qt-desktop

  Public
  The desktop Grassroots client application for running services on Grassroots servers

  C++

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

• grassroots-accessions-service

  Public
  A Grassroots service for managing and querying various different plant accessions

  C

  •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

• SingleCellSchemas

  Public
  For resources related to the EI Cellgen ISP, including metadata mappings and schemas for Single Cell Genomics and Spatial Transcriptomics experiments.

  sequencingschemassingle-cell+ 3

  sequencingschemassingle-cellsingle-cell-rna-seqspatial-transcriptomicsearlham-institute

  Python

  •

  Other

  •0•1•0•0•Updated Feb 13, 2026Feb 13, 2026

• grassroots-service-field-pathogenomics

  Public
  The Grassroots service for geolocation and dates of samples of crop pathogenomic data

  C

  •

  Apache License 2.0

  •1•2•0•0•Updated Feb 5, 2026Feb 5, 2026

• grassroots-build-tools

  Public
  Scripts to manage the building of the different Grassroots infrastructure components

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

• grassroots-installer

  Public
  Tools to automate the installation of Grassroots

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

• anndata_injection

  Public
  project to inject anndata files with metadata from COPO schema

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 30, 2026Jan 30, 2026

• COPO-schemas

  Public
  This repository provides a collection of schemas, or data objects, for representing different types of metadata.

  metadatavalidationschemas+ 7

  metadatavalidationschemasdata-standardsresearch-datachecklistscopolife-sciencecopo-projectmetadata-submission

  MIT License

  •0•1•0•0•Updated Jan 16, 2026Jan 16, 2026

• Scraper_sc

  Public
  This project automates the extraction of structured metadata from scientific papers in PDF format. Using the OpenAI GPT model, it populates a standardised Excel…

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

• knowledge_base

  Public
  EI specific documentation (induction materials, tool/method specific advice); contributions made by EI users.

  0•3•0•0•Updated Dec 18, 2025Dec 18, 2025

• earlham-galaxytools

  Public
  Galaxy tools and workflows developed at the Earlham Institute

  Python

  •

  MIT License

  •15•14•7•3•Updated Dec 8, 2025Dec 8, 2025

• COPO-ansible-deployment

  Public
  COPO - ansible deployment

  MIT License

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

• nanopore-mod-course-2024

  Public
  Contains materials used for the nanopore base modification course at the Earlham Institute that ran in 2024

  CSS

  •

  Other

  •119•1•0•0•Updated Nov 25, 2025Nov 25, 2025

• reposyncer

  Public
  GitHub workflow to sync various repo mirrors

  MIT License

  •2•0•0•0•Updated Nov 24, 2025Nov 24, 2025

• JP_PhD

  Public
  Additional material for Jess Peers' PhD thesis

  Python

  •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• 2025-11-04-earlham

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025