Introduction

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.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 data are available at Bioinformatics online.

Publications

  1. QuasR: quantification and annotation of short reads in R.
    Cite this
    Gaidatzis D, Lerch A, Hahne F, Stadler MB, 2015-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Dimos Gaidatzis
    Developer

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Switzerland

  2. Anita Lerch
    Developer

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Switzerland

  3. Florian Hahne
    Developer

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Switzerland

  4. Michael B Stadler
    Investigator

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Switzerland

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006896
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++, R
User InterfaceTerminal Command Line
Download Count0
Country/RegionSwitzerland
Submitted ByMichael B Stadler