Search across 65 species, 4,221 studies, 141,189 assays
Ensembl 99, Ensembl Genomes 46, WormBase ParaSite 14, EFO 3.10.0
Tools
iRAP: RNA-seq analysis tool
A flexible pipeline for RNA-seq analysis that integrates many existing tools for filtering and
mapping reads, quantifying expression and testing for differential expression. iRAP is used to
process all RNA-seq data in Expression Atlas.
Expression Atlas R Package on Bioconductor
Search and download pre-packaged data from Expression Atlas inside an R session. Raw counts are
provided for RNA-seq datasets and normalized intensities are available for microarray
experiments. Protocols describing how the data was generated and sample annotations are
contained within the downloaded R objects.
Expression Atlas Heatmap
You can embed the Expression Atlas heatmap as a JavaScript widget on your site. You can build it
from source or you can link directly to our built bundles. Instructions for both methods are
provided in the GitHub repository. It is strongly suggested that you go through all the examples
available in our showcase gallery .
Publications
Expression Atlas update: insights from sequencing data at both bulk and single cell level
Nucleic Acids Research, 01 January 2024.
Expression Atlas update: gene and protein expression in multiple species
Nucleic Acids Research, 24 November 2021.
RNA-Seq gene profiling – A systematic empirical comparison
PLoS One, 30 September 2014.