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 (eg 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. 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 stepby-step examples for typical work flows.

Contact: michael. stadler@ fmi. ch Supplementary information: Supplementary data are available at Bioinformatics online.