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CNVRuler specifications


Unique identifier OMICS_07495
Name CNVRuler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Yeun-Jun Chung <>

Publication for CNVRuler

CNVRuler citations


A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits

PMCID: 5417718
PMID: 28472114
DOI: 10.1371/journal.pone.0177014

[…] the cnvrs were determined by merging cnvs identified in two or more animals when the overlap is of at least 1 bp, according to the criteria proposed by redon et al. []. this merging was performed by cnvruler software []. regions of very low density of overlapping (recurrence parameter<0.1) were not used in the analyses for a more robust definition of the beginning and end regions., based […]


Genome Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle

PMCID: 4922624
PMID: 27348523
DOI: 10.1371/journal.pone.0157711

[…] cnvrs to establish relationships between structural genomic variation and mt., we used snp genotype data from 723 male nelore animals to infer 49,997 cnv calls and 2,649 cnvrs using penncnv [] and cnvruler [], respectively (see for genotyping, cnv calling and cnvr concatenation). the cnvrs represent 6.5% of the bos taurus genome (170.6 mb, genomic positions listed in ). the chromosomal […]


Identification of Copy Number Variations in Xiang and Kele Pigs

PMCID: 4740446
PMID: 26840413
DOI: 10.1371/journal.pone.0148565

[…] because the samples were obtained from multiple locations across congjiang county, china. thus, pedigree information was not incorporated into the analysis. moreover, the cnvs were aggregated using cnvruler software []., a hierarchical clustering analysis for all test samples was performed according to their cnv similarities. we first converted the copy number data to a scoring matrix […]


Identification of rare germline copy number variations over represented in five human cancer types

PMCID: 4381456
PMID: 25644941
DOI: 10.1186/s12943-015-0292-6

[…] studies with control (migen). cthe median, mean and standard deviation (sd) of the number of cnvs per individual are shown., to merge individual cnvs into common cnv regions (cnvr), we used cnvruler [], which is one of the few tools that integrate multiple methods for calculating cnvrs, with several statistical association tests and options for population stratification. to identify […]

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CNVRuler institution(s)
Integrated Research Center for Genome Polymorphism, Department of Microbiology, School of Medicine, Catholic University of Korea, Seoul, Korea

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