title: QuasR: quantification and annotation of short reads in R.
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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: 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.
authors.forename: Dimos
authors.initials: D
authors.lastname: Gaidatzis
authors.affiliation: 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.
authors.forename: Anita
authors.initials: A
authors.lastname: Lerch
authors.affiliation: 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.
authors.forename: Florian
authors.initials: F
authors.lastname: Hahne
authors.affiliation: 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.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Stadler
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D020451:Contig Mapping; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software