Repositories list

• bulk-quantification

  Public
  Bulk quantification workflow and supporting scripts

  00 forks•00 stars•00 issues•22 pull requests•Updated Aug 7, 2026Aug 7, 2026

• bulk-recalculations

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

  Python

  •11 fork•00 stars•1616 issues•33 pull requests•Updated Aug 7, 2026Aug 7, 2026

• atlas-analysis

  Public
  Scripts used in Atlas analysis pipelines

  R

  •00 forks•00 stars•33 issues•11 pull request•Updated Aug 7, 2026Aug 7, 2026

• atlas-schemas

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

  sqlsolrschemas+ 1

  sqlsolrschemassolrcloud

  Shell

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•22 pull requests•Updated Aug 6, 2026Aug 6, 2026

• atlas-annotations

  Public
  The pipeline producing bioentity annotations used in Expression Atlas searches

  Shell

  •11 fork•00 stars•1010 issues•99 pull requests•Updated Aug 4, 2026Aug 4, 2026

• atlas-gtex-bulk

  Public
  Atlas analysis for controlled-access GTEx bulk datasets

  rna-seqgtex

  rna-seqgtex

  Python

  •00 forks•00 stars•33 issues•11 pull request•Updated Aug 3, 2026Aug 3, 2026

• atlas-experiment-fetcher

  Public
  Fetches and formats GXA experiment data into structured YAML

  Python

  •00 forks•00 stars•11 issue•00 pull requests•Updated Aug 1, 2026Aug 1, 2026

• atlas-k8s-ci-environment

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

  k8s

  k8s

  Shell

  •

  Apache License 2.0

  •22 forks•22 stars•11 issue•00 pull requests•Updated Jul 30, 2026Jul 30, 2026

• atlas-faqs

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

  HTML

  •00 forks•00 stars•00 issues•11 pull request•Updated Jul 27, 2026Jul 27, 2026

• bulk-references

  Public
  Collection of scripts to manage references for bulk-rnaseq

  00 forks•00 stars•00 issues•11 pull request•Updated Jul 23, 2026Jul 23, 2026

• annotare2

  Public
  A web-based submission tool for ArrayExpress Archive

  Java

  •11 fork•66 stars•00 issues•55 pull requests•Updated Jul 19, 2026Jul 19, 2026

• magetab-validation-container

  Public
  A containerized command-line tool for validating MAGE-TAB formatted metadata files

  Dockerfile

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 13, 2026Jul 13, 2026

• galaxy-workflow-executor

  Public
  Utility scripts to run a Galaxy workflow on Galaxy through the CLI

  Python

  •00 forks•11 star•55 issues•22 pull requests•Updated Jul 10, 2026Jul 10, 2026

• scxa-workflows

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

  Shell

  •

  Apache License 2.0

  •22 forks•1414 stars•66 issues•11 pull request•Updated Jul 9, 2026Jul 9, 2026

• scxa-bundle-workflow

  Public
  Workflow for making bundles for Single-cell Expression Atlas

  Nextflow

  •00 forks•00 stars•11 issue•11 pull request•Updated Jul 9, 2026Jul 9, 2026

• scxa-aggregation-workflow

  Public
  Aggregation component for SCXA workflows

  Nextflow

  •11 fork•00 stars•00 issues•22 pull requests•Updated Jul 9, 2026Jul 9, 2026

• scxa-droplet-quantification-workflow

  Public
  Quantification component for droplet-based studies

  Nextflow

  •11 fork•55 stars•00 issues•11 pull request•Updated Jul 9, 2026Jul 9, 2026

• scxa-smartseq-quantification-workflow

  Public
  The SCXA smart-seq quantification workflow

  Nextflow

  •11 fork•00 stars•00 issues•11 pull request•Updated Jul 9, 2026Jul 9, 2026

• scxa-tertiary-workflow

  Public
  Tertiary component for SCXA workflows

  rna-seqpipelinenextflow+ 4

  rna-seqpipelinenextflowproteinsingle-cell10xgenomicssmartseq2

  Nextflow

  •

  MIT License

  •11 fork•11 star•1919 issues•55 pull requests•Updated Jul 9, 2026Jul 9, 2026

• annotare-help

  Public
  Help pages for functional genomics submissions

  HTML

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2026Jul 9, 2026

• atlas-web-bulk

  Public
  Bulk Expression Atlas web application

  javaspring

  javaspring

  Java

  •

  Apache License 2.0

  •22 forks•22 stars•5151 issues•33 pull requests•Updated Jul 7, 2026Jul 7, 2026

• atlas-web-core

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

  Java

  •11 fork•00 stars•66 issues•22 pull requests•Updated Jul 7, 2026Jul 7, 2026

• dependabot

  Public template
  🤖 Fork me to try out Dependabot

  Ruby

  •4.8k4.8k forks•00 stars•00 issues•66 pull requests•Updated Jun 24, 2026Jun 24, 2026

• atlas-conda

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

  Shell

  •00 forks•00 stars•00 issues•11 pull request•Updated Jun 22, 2026Jun 22, 2026

• internal-ExpressionAtlas

  Public
  Repository of Expression Atlas internal R package used for internal atlas processing.

  R

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jun 22, 2026Jun 22, 2026

• doi-gene-mining-pipeline

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2026Jun 18, 2026

• atlas-containers

  Public
  Common location to place our container definitions for integration with CI processes.

  Dockerfile

  •00 forks•00 stars•33 issues•11 pull request•Updated Jun 12, 2026Jun 12, 2026

• wf-bulk-indexing

  Public
  Running logic for the indexing tasks for Bulk Expression Atlas

  Python

  •11 fork•00 stars•00 issues•33 pull requests•Updated Jun 3, 2026Jun 3, 2026

• index-gxa

  Public
  Repository that handles indexing of GXA studies.

  Shell

  •00 forks•00 stars•22 issues•11 pull request•Updated Jun 2, 2026Jun 2, 2026

• index-bioentities

  Public
  Scripts to automate building and populating the bioentities collection

  Shell

  •00 forks•00 stars•00 issues•11 pull request•Updated Jun 2, 2026Jun 2, 2026