QuasR – Quantification and annotation of short reads in R

QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.

rna-seq

Availability and Implementation: QuasR is implemented in R and C/C++. Source code and binaries for major platforms (Linux, OS X and MS Windows) are available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/QuasR.html). The package includes a ‘vignette’ with step-by-step examples for typical work flows.

Contact: michael.stadler@fmi.ch

Gaidatzis D, Lerch A, Hahne F, Stadler MB. (2014) QuasR: Quantification and annotation of short reads in R. Bioinformatics [Epub ahead of print]. [article]

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