title: easyRNASeq: a bioconductor package for processing RNA-Seq data.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  delhomme@embl.de.
authors: Genome Biology Computational Support, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. delhomme@embl.de
authors: Nicolas
authors: N
authors: Delhomme
authors: Ismaël
authors: I
authors: Padioleau
authors: Eileen E
authors: EE
authors: Furlong
authors: Lars M
authors: LM
authors: Steinmetz
mesh_terms: D019295:Computational Biology / Q000379:methods; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA