QuasR: quantification and annotation of short reads in R

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology*
  • Contig Mapping*
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Sequence Analysis, DNA / methods*
  • Software*