shazam

February 20, 2016 Version 0.1.2

Somatic hypermutation analysis package.

Dependencies

R 3.1.2
R packages

• alakazam
• data.table
• doParallel
• dplyr
• foreach
• ggplot2
• iterators
• scales
• SDMTools
• seqinr
• stringi
• tidyr

Build Instructions

Install build dependencies:

install.packages(c("devtools", "roxygen2", "testthat", "knitr", "rmarkdown"))

Building with Rstudio:

• Build -> Configure Build Tools
• Check the Use devtools package functions option
• Check the Generate documentation with Roxygen option
• Select Configure... Roxygen options and check everything.
• Build -> Build and Reload

Building from the R console:

devtools::install_deps()
devtools::document()
devtools::build()
devtools::install()

Optionally, you can skip the vignettes:

devtools::build(vignettes=FALSE)