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easyRNASeq: a bioconductor package for processing RNA-Seq data.

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.

Pubmed ID: 22847932

Authors

  • Delhomme N
  • Padioleau I
  • Furlong EE
  • Steinmetz LM

Journal

Bioinformatics (Oxford, England)

Publication Data

October 1, 2012

Associated Grants

  • Agency: NIGMS NIH HHS, Id: R01 GM068717
  • Agency: NIGMS NIH HHS, Id: R01 GM068717

Mesh Terms

  • Computational Biology
  • RNA
  • Sequence Analysis, RNA
  • Software