CERENKOV
CERENKOV is a tool for the identification of functional noncoding single nucleotide polymorphism (SNP) in loci identified by genome-wide association studies (GWAS). The CERENKOV algorithm uses data-space geometric features and the xgboost classifier.
Topic
Molecular genetics, Genetic variation, DNA polymorphism
Detail
Operation: Nucleic acid sequence feature detection, SNP detection
Software interface: Command-line interface, R package
Language: R
License: Apache License 2.0
Cost: Free
Version name: -
Credit: The Medical Research Foundation of Oregon, Oregon State University, the PhRMA Foundation, the National Science Foundation.
Input: -
Output: -
Contact: yaoyao@oregonstate.edu | liuzhen@oregonstate.edu | weiq@oregonstate.edu | stephen.ramsey@oregonstate.edu | yaoyao@oregonstate.edu
Collection: -
Maturity: -
Publications
- CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.
- Yao Y, et al. CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. 2019; 20:63. doi: 10.1186/s12859-019-2637-4
- https://doi.org/10.1186/s12859-019-2637-4
- PMID: 30727967
- PMC: PMC6364436
Download and documentation
Documentation: https://github.com/ramseylab/cerenkov/blob/master/README.md
Home page: https://github.com/ramseylab/cerenkov
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