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

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, Rsamtools, as well as to perform differential gene expression analyses, e.g. DESeq, edgeR. However, the processing tasks lying in between these requires the precise interplay of many Bioconductor packages, e.g. Biostrings, IRanges or external solutions are to be sought.
The easyRNASeq is an R package that simplifies the processing of RNA sequencing data, hiding the complex interplay of the required packages behind a single functionality. 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

Reference:

easyRNASeq: a bioconductor package for processing RNA-Seq data. Delhomme N, Padioleau I, Furlong EE, Steinmetz L. Bioinformatics. 2012 Jul 30.

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