For better experience, turn on JavaScript!


modSaRa2

modSaRa2

modSaRa2 is an R package to identify copy number variable (CNV) segments in genomic data. modSaRa2 is an improved version of modSaRa by the integration of relative allelic intensity data to reduce noise.

Topic

Genetics; nucleic acid structure analysis

Details

  • Operation: Prediction and recognition
  • Software interface: Command-line user interface
  • Language: R;C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2+
  • Cost: Free
  • Version name: 1.0
  • Credit: The National Institute on Drug Abuse, National Science Foundation Grant DMS-1309507 and the internal fund from the University of South Carolina.
  • Contact: heping.zhang _at_ yale.edu
  • Collection: SaRa

Publications

Xiao F, Luo X, Hao N, Niu YS, Xiao X, Cai G, Amos CI, Zhang H "An accurate and powerful method for copy number variation detection" Bioinformatics. 2019 Jan 14 https://doi.org/10.1093/bioinformatics/bty1041
PMID: 30649252


Xiao F, Niu Y, Hao N, Xu Y, Jin Z, Zhang H "modSaRa: a computationally efficient R package for CNV identification." Bioinformatics. 2017 Aug 1;33(15):2384-2385. https://doi.org/10.1093/bioinformatics/btx212
PMID: 28453611
PMCID: PMC5860124


Niu YS, Zhang H "THE SCREENING AND RANKING ALGORITHM TO DETECT DNA COPY NUMBER VARIATIONS." Ann Appl Stat. 2012 Sep;6(3):1306-1326. https://doi.org/10.1214/12-AOAS539SUPP
PMID: 24069112
PMCID: PMC3779928


Hao N, Niu YS, Zhang H "Multiple Change-Point Detection via a Screening and Ranking Algorithm." Stat Sin. 2013 Jul 1;23(4):1553-1572. https://doi.org/10.5705/ss.2012.018s
PMID: 24489450
PMCID: PMC3902887


Download and documentation








If you find errors, please report here.