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QuasR

QuasR

QuasR is a tool to quantify and annotate reads from RNA-seq, ChIP-seq, and Bis-seq. The QuasR package has tools for all analysis steps from sequence read preprocessing, alignment, and quality control to quantification.

Topic

Sequencing; Genetics; Workflows; ChIP-seq; RNA-Seq; Microarray experiment

Details

  • Operation: Read pre-processing; Read mapping; Statistical calculation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.26.0
  • Maturity: Stable
  • Credit: Sybit, SystemsX.ch, the Novartis Research Foundation.
  • Contact: Michael Stadler michael.stadler _at_ fmi.ch
  • Collection: Bioconductor

Publications

Gaidatzis D, Lerch A, Hahne F, Stadler MB "QuasR: quantification and annotation of short reads in R." Bioinformatics. 2015 Apr 1;31(7):1130-2. 2014 Nov 21. https://doi.org/10.1093/bioinformatics/btu781
PMID: 25417205
PMCID: PMC4382904


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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