ArrayExpressHTS – A pipeline for RNA-seq data processing and quality assessment

ArrayExpressHTS is an R based pipeline for pre-processing, expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets. The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing gene or transcript measurements for downstream analysis along with web reports for data quality assessment. It may be run locally on a user’s own computer or remotely on a distributed R-cloud farm at the European Bioinformatics Institute. It can be used to analyse user’s own datasets or public RNA-seq datasets from the ArrayExpress Archive.

Availability: The R package is available at

Online documentation at


Goncalves A, Tikhonov A, Brazma A, Kapushesky M. (2011) A pipeline for RNA-seq data processing and quality assessment. Bioinformatics [Epub ahead of print]. [article]