Repositories list

• wf-bulk-indexing

  Public
  Running logic for the indexing tasks for Bulk Expression Atlas

  Python

  •1•0•0•3•Updated Aug 18, 2025Aug 18, 2025

• atlas-web-bulk

  Public
  Bulk Expression Atlas web application

  javaspring

  Java

  •

  Apache License 2.0

  •2•2•58•9•Updated Aug 15, 2025Aug 15, 2025

• atlas-gtex-bulk

  Public
  Atlas analysis for controlled-access GTEx bulk datasets

  rna-seqgtex

  Python

  •0•0•3•2•Updated Aug 15, 2025Aug 15, 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•5•1•Updated Aug 15, 2025Aug 15, 2025

• atlas-experiment-fetcher

  Public
  Fetches and formats GXA experiment data into structured YAML

  Python

  •0•0•1•0•Updated Aug 15, 2025Aug 15, 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•2•Updated Aug 13, 2025Aug 13, 2025

• atlas-experiment

  Public
  Experiment page for bulk Expression Atlas

  react

  HTML

  •0•0•0•1•Updated Aug 12, 2025Aug 12, 2025

• annotare-help

  Public
  Help pages for functional genomics submissions

  HTML

  •2•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• atlas-heatmap

  Public
  Heatmap visualizing bulk Expression Atlas data

  react

  JavaScript

  •2•8•2•0•Updated Aug 11, 2025Aug 11, 2025

• atlas-schemas

  Public
  Schemas for the database and SolrCloud servers used by Expression Atlas and Single Cell Expression Atlas

  sqlsolrschemas+ 1solrcloud

  Shell

  •

  Apache License 2.0

  •0•0•0•2•Updated Aug 11, 2025Aug 11, 2025

• atlas-annotations

  Public
  The pipeline producing bioentity annotations used in Expression Atlas searches

  Shell

  •1•0•10•6•Updated Aug 6, 2025Aug 6, 2025

• atlas-web-single-cell

  Public
  Single Cell Expression Atlas web application

  Java

  •

  Apache License 2.0

  •5•5•80•9•Updated Aug 1, 2025Aug 1, 2025

• atlas-bulk-differential-ot-export-wf

  Public
  0•0•0•1•Updated Jul 25, 2025Jul 25, 2025

• bulk-recalculations

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

  Python

  •1•0•16•2•Updated Jul 18, 2025Jul 18, 2025

• atlas-analysis

  Public
  Scripts used in Atlas analysis pipelines

  R

  •0•0•3•1•Updated Jul 18, 2025Jul 18, 2025

• atlas-release-notes

  Public
  Release notes for (Single Cell) Expression Atlas

  Shell

  •0•0•1•2•Updated Jul 18, 2025Jul 18, 2025

• atlas-faqs

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

  HTML

  •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

• data-exports-bulk

  Public
  Data export module for Atlas Prod

  Perl

  •

  MIT License

  •1•0•0•1•Updated Jul 11, 2025Jul 11, 2025

• atlas-bulk-baseline-ot-export-wf

  Public
  New baseline export for Open Targets (although it is meant as a general purpose export)

  Python

  •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

• container-galaxy-sc-tertiary

  Public
  Galaxy container for single cell RNA-Seq tertiary analysis tools

  Python

  •

  MIT License

  •15•17•28•11•Updated Jun 26, 2025Jun 26, 2025

• expression-atlas-curation-guide

  Public
  Curation rules and experiment inclusion criteria for the Expression Atlas

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

• atlas-components

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

  JavaScript

  •3•3•14•1•Updated Jun 4, 2025Jun 4, 2025

• atlas-bash-util

  Public
  Shell

  •0•0•3•1•Updated May 12, 2025May 12, 2025

• atlas-conda

  Public
  Internal conda recipes relevant for atlas but not of general interest to be in bioconda

  Shell

  •0•0•0•2•Updated May 2, 2025May 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 Apr 30, 2025Apr 30, 2025

• bioconductor-ExpressionAtlas

  Public
  Download datasets from EMBL-EBI Expression Atlas

  bioconductor

  R

  •1•1•3•2•Updated Apr 10, 2025Apr 10, 2025

• scxa-workflows

  Public
  Higher level repo for aggregating all of Atlas workflow logic for Single Cell

  Shell

  •

  Apache License 2.0

  •2•14•6•1•Updated Apr 1, 2025Apr 1, 2025

• scxa-tertiary-workflow

  Public
  Tertiary component for SCXA workflows

  rna-seqpipelinenextflow+ 4proteinsingle-cell10xgenomicssmartseq2

  Nextflow

  •

  MIT License

  •1•1•19•3•Updated Mar 31, 2025Mar 31, 2025

• atlas-help-pages

  Public
  HTML

  •

  GNU General Public License v3.0

  •2•0•0•1•Updated Mar 28, 2025Mar 28, 2025

• species-summary-panel

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

  JavaScript

  •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025