EBI Gene Expression Group

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anatomogram anatomogram Public

Anatomogram illustrating Expression Atlas experiments

JavaScript 50 20
scanpy-scripts scanpy-scripts Public

Scripts for using scanpy

Python 39 14
atlas atlas Public archive

Expression Atlas

Java 27 4
r-seurat-scripts r-seurat-scripts Public

Scripts to install as a Bioconda package for making workflows

R 18 4
container-galaxy-sc-tertiary container-galaxy-sc-tertiary Public

Galaxy container for single cell RNA-Seq tertiary analysis tools

Python 18 15
scxa-workflows scxa-workflows Public

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

Shell 14 2

Repositories

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

ebi-gene-expression-group/atlas-containers’s past year of commit activity

Dockerfile 0 0 3 2 Updated Mar 25, 2026
bulk-references Public
Collection of scripts to manage references for bulk-rnaseq

ebi-gene-expression-group/bulk-references’s past year of commit activity

0 0 0 1 Updated Mar 25, 2026
atlas-conda Public
Internal conda recipes relevant for atlas but not of general interest to be in bioconda

ebi-gene-expression-group/atlas-conda’s past year of commit activity

Shell 0 0 0 1 Updated Mar 25, 2026
atlas-web-bulk Public
Bulk Expression Atlas web application

ebi-gene-expression-group/atlas-web-bulk’s past year of commit activity

Java 2 Apache-2.0 2 51 7 Updated Mar 25, 2026
bulk-quantification Public
Bulk quantification workflow and supporting scripts

ebi-gene-expression-group/bulk-quantification’s past year of commit activity

0 0 0 2 Updated Mar 25, 2026
annotare-help Public
Help pages for functional genomics submissions

ebi-gene-expression-group/annotare-help’s past year of commit activity

HTML 0 2 0 2 Updated Mar 23, 2026
scxa-workflows Public
Higher level repo for aggregating all of Atlas workflow logic for Single Cell

ebi-gene-expression-group/scxa-workflows’s past year of commit activity

Shell 14 Apache-2.0 2 6 1 Updated Mar 23, 2026
scxa-tertiary-workflow Public
Tertiary component for SCXA workflows

ebi-gene-expression-group/scxa-tertiary-workflow’s past year of commit activity

Nextflow 1 MIT 1 19 (1 issue needs help) 4 Updated Mar 20, 2026
annotare2 Public
A web-based submission tool for ArrayExpress Archive

ebi-gene-expression-group/annotare2’s past year of commit activity

Java 6 1 0 6 Updated Mar 20, 2026
atlas-web-single-cell Public
Single Cell Expression Atlas web application

ebi-gene-expression-group/atlas-web-single-cell’s past year of commit activity

Java 6 Apache-2.0 5 77 2 Updated Mar 17, 2026