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    162 repositories

    • rfparser

      Public
      Parse ResearchFish publications to update CKAN
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 10, 2026Jan 10, 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 Jan 9, 2026Jan 9, 2026

    • eisca

      Public
      A single-cell RNA-seq pipeline aimed at covering all analysis stages from quantification and clustering to tertiary analyses.
      Nextflow
      •
      MIT License
      •1•2•2•0•Updated Jan 9, 2026Jan 9, 2026

    • 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 standards, ensuring data is discoverable, interoperable, and accessible. Submitted data is accessible via public repositories, promoting long-term preservation and reuse across systems.
      researchgenomicsomicsbiodiversitylife-sciencesmetadata-broker
      JavaScript
      •
      MIT License
      •2•5•0•11•Updated Jan 9, 2026Jan 9, 2026

    • COPO-schemas

      Public
      This repository provides a collection of schemas, or data objects, for representing different types of metadata.
      metadatavalidationschemasdata-standardsresearch-datachecklistscopolife-sciencecopo-projectmetadata-submission
      MIT License
      •0•1•0•0•Updated Jan 9, 2026Jan 9, 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.
      metadatasphinxreadthedocssphinx-documentationcopocopo-projectcopo-docs
      Python
      •
      Apache License 2.0
      •0•2•0•2•Updated Jan 8, 2026Jan 8, 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 workbook with metadata for single-cell RNA-seq studies. Each PDF is parsed and its contents used to fill out the appropriate fields across multiple Excel sheets, one per metadata category.
      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

    • 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 Dec 8, 2025Dec 8, 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

    • SingleCellSchemas

      Public
      For resources related to the EI Cellgen ISP, including metadata mappings and schemas for Single Cell Genomics and Spatial Transcriptomics experiments.
      sequencingschemassingle-cellsingle-cell-rna-seqspatial-transcriptomicsearlham-institute
      Python
      •
      Other
      •0•1•0•0•Updated Dec 3, 2025Dec 3, 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
      •117•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

    • grassroots-installer

      Public
      Tools to automate the installation of Grassroots
      Shell
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 24, 2025Nov 24, 2025

    • MARTi

      Public
      Metagenomic Analysis in Real Time
      Java
      •
      MIT License
      •3•0•0•0•Updated Nov 23, 2025Nov 23, 2025

    • JP_PhD

      Public
      Additional material for Jess Peers' PhD thesis
      Python
      •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • grassroots-lucene

      Public
      Lucene engine customised for Grassroots data
      Java
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 11, 2025Nov 11, 2025

    • grassroots_services_django_web

      Public
      JavaScript
      •1•0•0•10•Updated Oct 31, 2025Oct 31, 2025

    • 2025-11-04-earlham

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • grassroots-core

      Public
      The core libraries of the Grassroots infratructure
      C
      •
      Apache License 2.0
      •0•1•0•0•Updated Oct 27, 2025Oct 27, 2025

    • Aequatus

      Public
      Earlham Institute's Synteny Browser
      JavaScript
      •
      GNU General Public License v3.0
      •0•7•1•30•Updated Oct 26, 2025Oct 26, 2025

    • 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 Oct 25, 2025Oct 25, 2025

    • TGACBrowser

      Public
      TGAC's Genome Browser
      JavaScript
      •0•11•1•42•Updated Oct 22, 2025Oct 22, 2025

    • cvanmf

      Public
      (bi)crossvalidation for NMF rank selection, and visualisation/analysis tools
      Python
      •
      GNU General Public License v2.0
      •2•1•0•0•Updated Sep 21, 2025Sep 21, 2025

    • grassroots-service-search

      Public
      A service to search across all of the Grassroots data and tools
      C
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • grassroots-parental-genotype-service

      Public
      A Grassroots service to give parental cross information for given markers
      C
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • grassroots-service-gene-trees

      Public
      C
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • 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 Sep 16, 2025Sep 16, 2025

    • grassroots-brapi-module

      Public
      A wrapper for the Grassroots DFW Field Trial Service to give a BrAPI interface
      C
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 7, 2025Sep 7, 2025