Sunday, November 23, 2014

fwd: QuasR: Quantification and annotation of short reads in R

Fwd: please follow footer link

QuasR: Quantification and annotation of short reads in R: "

Summary: 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.

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

Supplementary Information: Supplementary data are available at Bioinformatics online.

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(Via Bioinformatics - Advance Access.)