Repositories list

• atlas-experiment-fetcher

  Public

  ebi-gene-expression-group/atlas-experiment-fetcher’s past year of commit activity
  Fetches and formats GXA experiment data into structured YAML

  Python

  •0•0•1•0•Updated Nov 15, 2025Nov 15, 2025

• bulk-quantification

  Public

  ebi-gene-expression-group/bulk-quantification’s past year of commit activity
  Bulk quantification workflow and supporting scripts

  0•0•0•1•Updated Nov 13, 2025Nov 13, 2025

• bulk-recalculations

  Public
  Snakemake workflow for new experiments processing, reprocessing and recalculations steps

  Python

  •1•0•16•3•Updated Nov 12, 2025Nov 12, 2025

• atlas-k8s-ci-environment

  Public
  Collection of Kubernetes manifests for CI of Expression Atlas web applications

  k8s

  Shell

  •

  Apache License 2.0

  •3•2•1•1•Updated Nov 11, 2025Nov 11, 2025

• scxa-workflows

  Public

  ebi-gene-expression-group/scxa-workflows’s past year of commit activity
  Higher level repo for aggregating all of Atlas workflow logic for Single Cell

  Shell

  •

  Apache License 2.0

  •2•14•6•1•Updated Nov 11, 2025Nov 11, 2025

• scxa-bundle-workflow

  Public
  Workflow for making bundles for Single-cell Expression Atlas

  Nextflow

  •0•0•1•0•Updated Nov 11, 2025Nov 11, 2025

• bulk-references

  Public

  ebi-gene-expression-group/bulk-references’s past year of commit activity
  Collection of scripts to manage references for bulk-rnaseq

  0•0•0•1•Updated Nov 10, 2025Nov 10, 2025

• index-scxa

  Public

  ebi-gene-expression-group/index-scxa’s past year of commit activity
  Schema and loading methods for scxa-analytics index

  Shell

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

• scxa-tertiary-workflow

  Public
  Tertiary component for SCXA workflows

  rna-seqpipelinenextflow+ 4proteinsingle-cell10xgenomicssmartseq2

  Nextflow

  •

  MIT License

  •1•1•19•4•Updated Oct 28, 2025Oct 28, 2025

• atlas-annotations

  Public

  ebi-gene-expression-group/atlas-annotations’s past year of commit activity
  The pipeline producing bioentity annotations used in Expression Atlas searches

  Shell

  •1•0•10•7•Updated Oct 24, 2025Oct 24, 2025

• solr-bulk

  Public
  Scripts to create and manage Solr collections used by (bulk) Expression Atlas

  Shell

  •0•0•1•1•Updated Oct 23, 2025Oct 23, 2025

• atlas-heatmap

  Public
  Heatmap visualizing bulk Expression Atlas data

  react

  JavaScript

  •2•8•3•1•Updated Oct 20, 2025Oct 20, 2025

• scanpy-scripts

  Public
  Scripts for using scanpy

  Python

  •

  Apache License 2.0

  •13•38•12•4•Updated Oct 20, 2025Oct 20, 2025

• atlas-release-notes

  Public
  Release notes for (Single Cell) Expression Atlas

  Shell

  •0•0•1•1•Updated Oct 17, 2025Oct 17, 2025

• atlas-faqs

  Public
  This is the repo containing FAQs for both bulk and single cell expression atlas

  HTML

  •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

• atlas-help-pages

  Public
  HTML

  •

  GNU General Public License v3.0

  •2•0•0•1•Updated Oct 16, 2025Oct 16, 2025

• atlas-web-core

  Public
  Business logic for single cell and bulk Expression Atlas and for the up-and-coming Expression Atlas API

  Java

  •1•0•6•2•Updated Oct 16, 2025Oct 16, 2025

• atlas-web-bulk

  Public
  Bulk Expression Atlas web application

  javaspring

  Java

  •

  Apache License 2.0

  •2•2•51•8•Updated Oct 16, 2025Oct 16, 2025

• atlas-analysis

  Public
  Scripts used in Atlas analysis pipelines

  R

  •0•0•3•2•Updated Oct 7, 2025Oct 7, 2025

• isl_refs_to_refgenie

  Public
  Build refgenie assets from existing ISL reference configs

  Nextflow

  •1•1•0•1•Updated Oct 6, 2025Oct 6, 2025

• rnaseq

  Public
  RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control

  Nextflow

  •

  MIT License

  •813•0•0•0•Updated Oct 3, 2025Oct 3, 2025

• atlas-components

  Public
  Front end components of Expression Atlas and Single Cell Expression Atlas

  JavaScript

  •3•3•14•0•Updated Oct 2, 2025Oct 2, 2025

• atlas-bash-util

  Public
  Shell

  •0•0•3•1•Updated Oct 2, 2025Oct 2, 2025

• scxa-control-workflow

  Public
  Master Nextflow workflow for running each component of the SMART-seq and droplet SCXA pipelines

  R

  •2•4•4•1•Updated Sep 30, 2025Sep 30, 2025

• index-bioentities

  Public
  Scripts to automate building and populating the bioentities collection

  Shell

  •0•0•0•1•Updated Sep 29, 2025Sep 29, 2025

• species-summary-panel

  Public
  Species panel for bulk Expression Atlas and Single Cell Expression Atlas

  JavaScript

  •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

• experiments-summary-panel

  Public
  Experiments panel for bulk Expression Atlas and Single Cell Expression Atlas

  JavaScript

  •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

• atlas-experiment

  Public
  Experiment page for bulk Expression Atlas

  react

  HTML

  •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

• atlas-web-single-cell

  Public
  Single Cell Expression Atlas web application

  Java

  •

  Apache License 2.0

  •5•5•77•8•Updated Sep 18, 2025Sep 18, 2025

• bioconductor-ExpressionAtlas

  Public
  Download datasets from EMBL-EBI Expression Atlas

  bioconductor

  R

  •1•1•3•1•Updated Sep 8, 2025Sep 8, 2025