denovolyzeR statistics

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Mutational signature detection

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denovolyzeR specifications

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Information

Unique identifier	OMICS_16468
Name	denovolyzeR
Software type	Package/Module
Interface	Command line interface
Restrictions to use	None
Operating system	Unix/Linux, Mac OS, Windows
Programming languages	R
License	GNU General Public License version 3.0
Computer skills	Advanced
Version	0.2.0
Stability	Stable
Requirements	rmarkdown, knitr, R(≥3.1.0), dplyr(≥0.3), reshape2(≥1.4)
Source code URL	https://cran.r-project.org/src/contrib/denovolyzeR_0.2.0.tar.gz
Maintained	Yes

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Documentation

Documentation: https://cran.r-project.org/web/packages/denovolyzeR/denovolyzeR.pdf

Maintainer

James Ware <>

Publication for denovolyzeR

Interpreting de novo Variation in Human Disease Using denovolyzeR.

2015 Curr Protoc Hum Genet

PMCID: 4606471

PMID: 26439716

DOI: 10.1002/0471142905.hg0725s87

denovolyzeR in publications

(3)

Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

PMCID: 5675000

PMID: 28991257

DOI: 10.1038/ng.3970

[…] using the approach detailed above. enrichment was calculated as the number of observed damaging genotypes/variants divided by the expected number of damaging genotypes/variants., the r package ‘denovolyzer’ was used for the analysis of dnms based on a mutation model developed previously, . the probability of observing a dnm in each gene was derived as described previously, except […]

Mutations in HECW2 are associated with intellectual disability and epilepsy

PMCID: 5099177

PMID: 27334371

DOI: 10.1136/jmedgenet-2016-103814

[…] two or more variants with one inherited from each parent, and where no parent carried both variants, was identified. to calculate the probability of mutations in the hecw2 gene the r library denovolyzer was used., dnms were validated by sanger sequencing using standard protocols. each validated variant was interpreted using the american college of medical genetics and genomics (acmg) […]

Two locus inheritance of non syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles

PMCID: 5045293

PMID: 27606499

DOI: 10.7554/eLife.20125.029

[…] 2.10.7554/elife.20125.009figure 2—figure supplement 1.10.7554/elife.20125.010figure 2—figure supplement 2.10.7554/elife.20125.011table 2.probabilities calculated from the poisson distribution using denovolyzer. the probability of observing at least 2 lof and 1 missense mutation in smad6 was 3.6 ×10−9 via fisher’s method., 10.7554/elife.20125.009figure 2—figure supplement 1., […]

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denovolyzeR funding source(s)

Supported by the NIHR Biomedical Research Unit in Cardiovascular Disease at Royal Brompton & Harefield NHS Foundation Trust and Imperial College London, Academy of Medical Sciences, Wellcome Trust, British Heart Foundation Arthritis Research U.K., Fondation Leducq, an HICF award from Wellcome Trust and Department of Health, the John S. LaDue Fellowship at Harvard Medical School, and grants R01MH089208 (NIH) and 1U01MH100229-01 (NIH/NIMH).

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