ichorCNA

Option 1 (Recommended)

Using R devtools

install.packages("devtools")
library(devtools)
install_github("broadinstitute/ichorCNA")

Option 2

Manual installation

1. Checkout the latest release of ichorCNA from GitHub

    git clone [email protected]:broadinstitute/ichorCNA.git  
   

2. Install R dependencies (in R-3.6.0 or later)

    ## install from CRAN
    install.packages("plyr") 
    ## install packages from
    source("https://bioconductor.org/biocLite.R")
    BiocManager::install("HMMcopy")  
    BiocManager::install("GenomeInfoDb")  
    BiocManager::install("GenomicRanges")  
   

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/ or https://github.com/shahcompbio/hmmcopy_utils . Please follow instructions on the HMMcopy website.