The Cambridge Portal of the Human Cell Atlas is a joint initiative between groups at EMBL-EBI and the Wellcome Sanger Institute. The project analyses, visualises and provides tools for exploration of single cell RNA-Seq data generated by the international Human Cell Atlas initiative, as well as other projects on human tissue. The portal is managed by the Gene Expression Team at EMBL-EBI in collaboration with the Wellcome Sanger Institute Cellular Genetics Programme.


Single Cell Expression Atlas provides access to the analysis results of 18 data sets from the Human Cell Atlas and 52 data sets in Homo sapiens studies which comprise samples from different organs and tissues.

All studies have been re-analysed using our standardised pipeline (SCXA-Workflows). Pipelines and web services are being developed by the Gene Expression Team at EMBL-EBI, funded by Wellcome and the Chan Zuckerberg Initiative.


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.

SCXA-Workflows on the Galaxy Human Cell Atlas project

scmap: projecting samples on to a reference
A fast method for identifying the closest matching cluster or cell in the Atlas to a new sample.

Single Cell Expression Atlas t-SNE widget
An easy-to-embed React component to visualise t-SNE plots from Single Cell Expression Atlas.