Repositories list

• rfparser

  Public
  Parse ResearchFish publications to update CKAN

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 29, 2025Jun 29, 2025

• grassroots_services_django_web

  Public
  JavaScript

  •1•0•0•10•Updated Jun 28, 2025Jun 28, 2025

• reposyncer

  Public
  GitHub workflow to sync various repo mirrors

  MIT License

  •2•0•0•0•Updated Jun 27, 2025Jun 27, 2025

• grassroots-server-apache-httpd

  Public
  The Apache httpd server module for the Grassroots infrastructure

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

• 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.

  researchgenomicsomics+ 3biodiversitylife-sciencesmetadata-broker

  JavaScript

  •

  MIT License

  •2•2•0•0•Updated Jun 26, 2025Jun 26, 2025

• COPO-schemas

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

  metadatavalidationschemas+ 7data-standardsresearch-datachecklistscopolife-sciencecopo-projectmetadata-submission

  MIT License

  •0•1•0•0•Updated Jun 26, 2025Jun 26, 2025

• 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•1•2•0•Updated Jun 24, 2025Jun 24, 2025

• 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+ 4sphinx-documentationcopocopo-projectcopo-docs

  Python

  •

  Apache License 2.0

  •0•2•0•2•Updated Jun 20, 2025Jun 20, 2025

• 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 Jun 17, 2025Jun 17, 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-cell+ 3single-cell-rna-seqspatial-transcriptomicsearlham-institute

  CSS

  •

  MIT License

  •0•1•0•0•Updated Jun 16, 2025Jun 16, 2025

• 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 Jun 15, 2025Jun 15, 2025

• grassroots-web-portal-static-onepage

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Jun 9, 2025Jun 9, 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 May 23, 2025May 23, 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 May 23, 2025May 23, 2025

• eista

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

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated May 16, 2025May 16, 2025

• grassroots-core

  Public
  The core libraries of the Grassroots infratructure

  C

  •

  Apache License 2.0

  •0•1•0•0•Updated May 1, 2025May 1, 2025

• grassroots-user-docs

  Public
  HTML

  •0•0•0•0•Updated May 1, 2025May 1, 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 Apr 28, 2025Apr 28, 2025

• grassroots-accessions-service

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

  C

  •0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

• 2025-06-10-earlham

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Apr 15, 2025Apr 15, 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 Apr 13, 2025Apr 13, 2025

• JP_PhD

  Public
  Additional material for Jess Peers' PhD thesis

  0•0•0•0•Updated Apr 3, 2025Apr 3, 2025

• EuropeanPolecatPopGen

  Public
  R

  •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

• earlham-galaxytools

  Public
  Galaxy tools and workflows developed at the Earlham Institute

  Python

  •

  MIT License

  •14•14•7•3•Updated Mar 31, 2025Mar 31, 2025

• TGACBrowser

  Public
  TGAC's Genome Browser

  JavaScript

  •0•10•1•32•Updated Mar 26, 2025Mar 26, 2025

• Aequatus

  Public
  Earlham Institute's Synteny Browser

  JavaScript

  •

  GNU General Public License v3.0

  •0•7•1•23•Updated Mar 23, 2025Mar 23, 2025

• grassroots-lucene

  Public
  Lucene engine customised for Grassroots data

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 17, 2025Mar 17, 2025

• COPO-ansible-deployment

  Public
  COPO - ansible deployment

  MIT License

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• LR_scRNAseq_Scoones_etal

  Public
  Repo contains scripts and links to Scoones et al: long-read scRNAseq transcriptomics comparison study

  MIT License

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• grassroots-service-users-groups

  Public
  A service to manage the authorization of users and groups within Grassroots

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 8, 2025Mar 8, 2025