Curr Protoc Hum Genet. 2015 Oct 6;87:7.25.1-15. doi: 10.1002/0471142905.hg0725s87.
This repo contains source code to produce the above methods paper, which describes the denovolyzeR software package, and its application for the analysis of de novo variants identified in human exome sequencing.
denovolyzeR is an R package, avaiable from CRAN.
The published manuscript is available through the journal webpage, PubMed, or PubMed Central (from Oct 6, 2016). If you don't have access, then [click here](mailto:j.ware@imperial.ac.uk?subject=denovolyzeR cphg reprint request&body=I think denovolyzeR is the best thing since sliced bread. Please send me a copy of your manuscript.) to request a pre-print from the authors.
Further information on the denovolyzeR software is located at http://denovolyzer.org.
The manuscript is authored in rmarkdown, compiled using knitr, and output as a word .docx file
- template.docx is a template for document formatting
- denovolyzerManuscriptReferences is an endnote library containing necessary references to format the bibliography in word after it is compiled by R.
(in subsequent manuscripts authored in R we have moved to the knitcitations package: an open source and more readily reproducible option. This also uses flat file formats that play more nicely with git version control)