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Updated: May 20, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
Published on: November 7, 2025
easyRNASeq: a bioconductor package for processing RNA-Seq data
Nicolas Delhomme1, Ismaël Padioleau, Eileen E Furlong
1Genome Biology Computational Support, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. delhomme@embl.de
Motivation:
RNA sequencing is becoming a standard for expression profiling experiments and many tools have been developed in the past few years to analyze RNA-Seq data. Numerous 'Bioconductor' packages are available for next-generation sequencing data loading in R, e.g. ShortRead and Rsamtools as well as to perform differential gene expression analyses, e.g. DESeq and edgeR. However, the processing tasks lying in between these require the precise interplay of many Bioconductor packages, e.g. Biostrings, IRanges or external solutions are to be sought.
Results:
We developed 'easyRNASeq', an R package that simplifies the processing of RNA sequencing data, hiding the complex interplay of the required packages behind a single functionality.
Availability:
The package is implemented in R (as of version 2.15) and is available from Bioconductor (as of version 2.10) at the URL: http://bioconductor.org/packages/release/bioc/html/easyRNASeq.html, where installation and usage instructions can be found.
Contact:
delhomme@embl.de.
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