denovolyzeR: an R package for the statistical analysis of de novo variants

This repository is the home of denovolyzeR, an R implementation of a statistical framework for the analysis of de novo genetic variants.

The statistical framework is published in Nature Genetics. To cite the R package, please cite our manuscript in Current Protocols in Human Genetics, also available on PubMed Central, as follows:

Ware, J.S., Samocha, K.E., Homsy, J., and Daly, M.J. 2015. Interpreting de novo variation in human disease using denovolyzeR. Curr. Protoc. Hum. Genet. 87:7.25.1-7.25.15. doi: 10.1002/0471142905.hg0725s87

The functions in this package calculate whether a study population carry more de novo variants than expected.

The latest released version can be installed from CRAN with

install.packages("denovolyzeR")

The latest development version can be installed from GitHub using devtools:

## Check whether devtools is installed
"devtools" %in% installed.packages()

## install devtools if required
install.packages("devtools")

## install denovolyzeR
library(devtools)
install_github("jamesware/denovolyzeR")

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