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QuasR: quantification and annotation of short reads in R
Dimos Gaidatzis1, Anita Lerch1, Florian Hahne2
1Friedrich 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.
Unlabelled:
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.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
