denovolyzeR is an R package for the analysis of de novo (sporadic) genetic variants, using a statistical framework described and validated by Samocha et al. Briefly, for each gene we derive the expected number of de novo events in a given population based on the mutability of the gene and the number of individuals sequenced, compare the observed number of de novos against expectation using a Poisson framework, and determine whether there is an excess of de novo events in a given variant class, gene, or pathway.

This approach has been applied to explore the role of de novo variants in a number of contexts, including autism spectrum disorders (Samocha et al Nature Genetics 2014) and congenital heart disease (Homsy et al Science 2015).

If using this software, please cite:
Curr Protoc Hum Genet. 2015;87:7.25.1-15. doi: 10.1002/0471142905.hg0725s87.

For a worked example of a typical de novo analysis using denovolyzeR, see the denovolyzeR package vignette.


The latest released version can be installed from CRAN:



The latest development version can be installed from GitHub. One simple approach uses devtools:

## Install devtools if not already installed
if(!"devtools" %in% installed.packages()){

## install denovolyzeR

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References and resources

Alternative mutational probability tables that can be downloaded for use with denovolyzeR can be found here.