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CNVRuler specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Yeun-Jun Chung

Publication for CNVRuler

CNVRuler citations

 (4)
library_books

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

2017
PLoS One
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. […]

library_books

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

2016
PLoS One
PMCID: 4922624
PMID: 27348523
DOI: 10.1371/journal.pone.0157711

[…] 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 proport […]

library_books

Identification of Copy Number Variations in Xiang and Kele Pigs

2016
PLoS One
PMCID: 4740446
PMID: 26840413
DOI: 10.1371/journal.pone.0148565

[…] s 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 []. […]

library_books

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

2015
Mol Cancer
PMCID: 4381456
PMID: 25644941
DOI: 10.1186/s12943-015-0292-6

[…] Illustrative examples of germline CNVRs are shown in Figure  with the remaining CNVRs (in Table ) illustrated in (Additional file : Figure S1). CNVRuler (v1.3) was used to merge individual CNVs into common CNV regions (CNVR) for each cancer and control set []. CNVRs that did not have a recurrence of > 0.1 were filtered from the list. CNVR fre […]

Citations

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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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