Repositories list

• 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 17, 2025Feb 17, 2025

• grassroots-core

  Public
  The core libraries of the Grassroots infratructure

  C

  •

  Apache License 2.0

  •0•1•0•0•Updated Feb 17, 2025Feb 17, 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•1•0•0•Updated Feb 17, 2025Feb 17, 2025

• earlham-galaxytools

  Public
  Galaxy tools and workflows developed at the Earlham Institute

  Python

  •

  MIT License

  •14•14•7•4•Updated Feb 17, 2025Feb 17, 2025

• rfparser

  Public
  Parse ResearchFish publications to update CKAN

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 16, 2025Feb 16, 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 Feb 13, 2025Feb 13, 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 Feb 12, 2025Feb 12, 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•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• cvanmf

  Public
  (bi)crossvalidation for NMF rank selection, and visualisation/analysis tools

  Python

  •

  GNU General Public License v2.0

  •1•1•0•0•Updated Feb 9, 2025Feb 9, 2025

• grassroots-accessions-service

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

  C

  •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

• TransfurOCR

  Public
  Transferring open chromatin predictions across mammals

  0•0•0•0•Updated Jan 13, 2025Jan 13, 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

  •114•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• grassroots_services_django_web

  Public
  JavaScript

  •1•0•0•10•Updated Dec 18, 2024Dec 18, 2024

• 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•0•0•Updated Dec 12, 2024Dec 12, 2024

• Aequatus

  Public
  Earlham Institute's Synteny Browser

  JavaScript

  •

  GNU General Public License v3.0

  •0•7•1•22•Updated Dec 5, 2024Dec 5, 2024

• reposyncer

  Public
  GitHub workflow to sync various repo mirrors

  MIT License

  •2•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• TGACBrowser

  Public
  TGAC's Genome Browser

  JavaScript

  •0•10•1•31•Updated Dec 2, 2024Dec 2, 2024

• 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 Nov 28, 2024Nov 28, 2024

• grassroots-service-polymarker

  Public
  The Polymarker service for the Grassroots infrastructure.

  C

  •

  Apache License 2.0

  •0•2•0•0•Updated Nov 24, 2024Nov 24, 2024

• grassroots-user-docs

  Public
  HTML

  •0•0•0•0•Updated Nov 24, 2024Nov 24, 2024

• grassroots-docs

  Public
  Documentation about the Grassroots Infrastructure

  JavaScript

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 24, 2024Nov 24, 2024

• grassroots-client-frictionless-data

  Public
  A tool to extract the resources from a Grassroots Frictionless Data Package

  C

  •

  Apache License 2.0

  •0•2•0•0•Updated Nov 24, 2024Nov 24, 2024

• grassroots-server-apache-httpd

  Public
  The Apache httpd server module for the Grassroots infrastructure

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 24, 2024Nov 24, 2024

• grassroots-tutorials

  Public
  A set of tutorials on using the various parts of Grassroots

  0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• 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 Nov 10, 2024Nov 10, 2024

• EDP

  Public
  mainline production repository for EDP

  JavaScript

  •

  MIT License

  •2•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• simple_templates

  Public
  A module to get the correct data for a project on the opendata portal

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• opendata-projects

  Public
  A tool to set the iRODS metadata from a projects store

  Python

  •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• QCPipeline

  Public
  QC pipeline for genome assemblies

  Shell

  •

  MIT License

  •2•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• Basecall2Assembly

  Public
  Snakemake pipeline that takes raw ONT and generates an assembly

  Python

  •

  MIT License

  •2•0•0•0•Updated Oct 25, 2024Oct 25, 2024