denovolyzeR statistics

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denovolyzeR specifications


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
rmarkdown, knitr, R(≥3.1.0), dplyr(≥0.3), reshape2(≥1.4)
Source code URL
Maintained Yes



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  • person_outline James Ware <>

Publication for denovolyzeR

denovolyzeR in publications

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 […]

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) […]

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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