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.
RNASeq-er API: a gateway to systematically updated analysis of public RNA-Seq data
The RNASeq-er REST API provides easy access to the results of the systematically updated and
continually growing analysis of public RNA-seq data in the European Nucleotide Archive (ENA).
The analysis of each sequencing run is performed by the EMBL-EBI's Gene Expression Team using
the iRAP pipeline (see above).
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
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 .
Expression Atlas update: gene and protein expression in multiple species
Nucleic Acids Research, 24 November 2021.
The RNASeq-er API – A gateway to systematically updated analysis of public RNA-seq data
Bioinformatics, 22 March 2017.
RNA-Seq gene profiling – A systematic empirical comparison
PLoS One, 30 September 2014.