Inferring balanced integer cancer genome graphs using mixed integer programming analysis of read depth and junction patterns in WGS data. .
- Install dependent packages and latest Bioconductor (if you haven't already)
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
biocLite("DNAcopy")
- Install devtools from CRAN (if you don't have it already)
install.packages('devtools')
install.packages('slam')
install.packages('Rcplex')
## Requires IBM ILOG CPLEX: install the community version, Download Rcplex source,
## note the include dir, and build Rcplex from source if auto install fails
## R CMD INSTALL --configure-args="--with-cplex-dir=/Applications/CPLEX_Studio_Community128/cplex" Rcplex_0.3-3.tar.gz
- Install dependent mskilab dependencies
devtools::install_github('mskilab/gUtils')
devtools::install_github('gTrack')
devtools::install_github('mskilab/gGnome')
- Install JaBbA
devtools::install_github('mskilab/JaBbA)