ParseCNV protocols

View ParseCNV computational protocol

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ParseCNV specifications

Information


Unique identifier OMICS_02566
Name ParseCNV
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Joseph Glessner <>

Publication for ParseCNV

ParseCNV in pipelines

 (2)
2016
PMCID: 4701378
PMID: 26730743
DOI: 10.1371/journal.pone.0145774

[…] using plink v.1.07 was carried out to assess the frequency difference between npc cases and healthy controls using gender and age as covariates. gene-based association was carried out using parsecnv v.17 []. gwama v.1.4 [] was used for i2 heterogeneity analysis. g*power v.3.1.9.2 was employed for power analysis for z tests logistic regression, using post-hoc computation of achieved […]

2016
PMCID: 5073740
PMID: 27769252
DOI: 10.1186/s12894-016-0180-4

[…] we removed all samples that deviated from the means of the first or second mds components by more than 3 standard deviations (sd). we also used a sample quality control function implemented in the parsecnv software package [, ] and removed samples with (1) high intensity noise (measured by sdlrr (sd of lrr) > mean +3 sd); (2) extreme intensity waviness (measured by more than 3 sd of mean […]


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ParseCNV in publications

 (9)
PMCID: 5709845
PMID: 29191242
DOI: 10.1186/s13073-017-0494-1

[…] probes., all qc steps were performed for cases and controls together in each cohort. about 20% of samples in each cohort were excluded during qc filtering., fisher exact test implemented in software parsecnv [] was used to conduct the cnv association analysis on each of the individual cohorts chop scz, chop asd, chop adhd, and depression. it was also used to compare cnv frequency between cases […]

PMCID: 5431949
PMID: 28496102
DOI: 10.1038/s41598-017-01896-w

[…] absolute cnv counts and genomic length, and then proceeded to perform association analysis between chd phenotype and cnvs. to minimize false positives, a combination of penncnv for cnv detection and parsecnv for association study, followed by a validation of the cnvs with a second independent technique was chosen, . results indicated that a microduplication in the first three exons of kat8 […]

PMCID: 5073740
PMID: 27769252
DOI: 10.1186/s12894-016-0180-4

[…] after sample quality control, gene- and cnv-based association tests were performed using cleaned data from group 1 (493 cases and 1586 controls) and group 2 (307 cases and 1102 controls) using parsecnv software. meta-analysis was performed using gene-based test results as input to identify significant genes, and cnvs in or around significant genes were identified in cnv-based association […]

PMCID: 4701378
PMID: 26730743
DOI: 10.1371/journal.pone.0145774

[…] using plink v.1.07 was carried out to assess the frequency difference between npc cases and healthy controls using gender and age as covariates. gene-based association was carried out using parsecnv v.17 []. gwama v.1.4 [] was used for i2 heterogeneity analysis. g*power v.3.1.9.2 was employed for power analysis for z tests logistic regression, using post-hoc computation of achieved […]

PMCID: 4543987
PMID: 26292654
DOI: 10.1038/srep13391

[…] removed., after qc, we performed pca based on snp genotypes of a set of ld (linkage disequilibrium)-pruned snps using software eigenstrat., we tested cnv association with t2d case control status via parsecnv which uses an unbiased segment-based scoring approach to identify cnv regions (cnvrs) associated with the disease status. briefly, for each snp, cnv frequency between cases and controls […]


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ParseCNV institution(s)
Department of Pediatrics, Division of Human Genetics, The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA

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