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ORE

ORE

ORE (Outlier-RV Enrichment) is a tool for the identification of non-coding rare variants in RNA-seq data. The ORE algorithm detects biologically significant outliers having more or less rare variants than expected by chance. Requires: Python >= 3.5.0, bedtools >= 2.2.7.0, samtools >= 1.3, and bcftools >=1.6.

Topic

Genetic variation; RNA-seq

Details

  • Operation: Genetic variation analysis
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Mac OS X, Linux
  • License: The MIT License
  • Cost: Free
  • Version name: 0.2.1
  • Maturity: Emerging
  • Credit: the National Institute of Dental and Craniofacial Research Interdisciplinary Training in Systems and Developmental Biology and Birth Defects, Mount Sinai Medical Scientist Training Program, ational Heart, Lung, and Blood Institute (NHLBI).
  • Contact: Felix Richter felix.richter _at_ icahn.mssm.edu | B. D. Gelb bruce.gelb _at_ mssm.edu
  • Collection: -

Publications

Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, Morton SU, DePalma S, Gorham J, Kitaygorodksy A, Porter GA, Giardini A, Shen Y, Chung WK, Seidman JG, Seidman CE, Schadt EE, Gelb BD "ORE identifies extreme expression effects enriched for rare variants." Bioinformatics. 2019 Oct 15;35(20):3906-3912. https://doi.org/10.1093/bioinformatics/btz202
PMID: 30903145
PMCID: PMC6792115


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