Bioinformatics. 2015 Apr 1;31(7):1130-2. doi: 10.1093/bioinformatics/btu781. Epub 2014 Nov 21.

QuasR: quantification and annotation of short reads in R.

Gaidatzis D¹, Lerch A¹, Hahne F², Stadler MB¹.

Author information

1: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland.
2: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland.

Abstract

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.