Search across 21 species, 384 studies, 10,051,914 cells
Ensembl 104, Ensembl Genomes 51, WormBase ParaSite 15, EFO 3.10.0
Tools
SCXA-Workflows
A flexible pipeline for Single Cell RNA-seq analysis that integrates many existing tools for
filtering and mapping reads, quantifying expression, clustering, finding marker genes and variable
genes. The workflows maximize reproducibility by making use of Bioconda, Biocontainers, NextFlow
and Galaxy. They can be run on the cloud, local machines or local premises.
Single Cell Expression Atlas t-SNE plot widget
You can embed the Single Cell Expression Atlas t-SNE plots as a JavaScript widget on your site.
There are detailed instructions to integrate the plots in your service in the linked GitHub
repository.
How to cite Expression Atlas
If you’re using Expression Atlas in your research, please consider citing our most recent update in Nucleic Acids Research:
Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration
Nucleic Acids Research, 10 December 2025.
If you would like to reference specific historical updates or methodology, you can also cite:
Expression Atlas update: insights from sequencing data at both bulk and single cell level
Nucleic Acids Research, 22 November 2023.
Expression Atlas update: gene and protein expression in multiple species
Nucleic Acids Research, 24 November 2021.
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
Nature Methods, 29 March 2021.