Installation

ichorCNA

Option 1 (Recommended)

Using R devtools

install.packages("devtools")
library(devtools)
install_github("broadinstitute/ichorCNA", "--no-docs")

Option 2

Manual installation

1. Checkout the latest release of ichorCNA from GitHub

    git clone git@github.com:broadinstitute/ichorCNA.git  
   

2. Install R dependencies (in R)

    ## install from CRAN
    install.packages("plyr") # version > 1.8.4
    ## install packages from
    source("https://bioconductor.org/biocLite.R")
    biocLite("HMMcopy") # version >= 1.14.0
    biocLite("GenomeInfoDb") # version >= 1.8.7 
   

3. Install the ichorCNA R package

    ## from the command line and in the directory where ichorCNA github was cloned.
    R CMD INSTALL ichorCNA   
   

HMMcopy (for readCounter)

Install the HMMcopy suite from http://shahlab.ca/projects/hmmcopy_utils/
Please follow instructions on the HMMcopy website.