Third Party Software Dependencies

Omics Pipe is dependent upon several third-party software packages. Before running Omics Pipe, please install all of the required tools for the pipeline you will be running (see below) as `Modules`_ on your local cluster. If you are running the AWS distribution, all third party software is already installed.

R Packages Needed

In R, you can cut and copy this to install all required packages:

install.packages(c("bibtex",    "AnnotationDbi", "cluster", "cummeRbund", "data.table", "DBI", "DESeq2", "devtools",    "dplyr",        "gdata",
"ggplot2", "graphite", "igraph", "KEGGREST","knitr", "knitrBootstrap",  "lattice", "locfit",    "pamr", "pander",       "pathview",
"plyr","RColorBrewer","Rcpp",   "RcppArmadillo", "RCurl", "ReactomePA", "RefManageR","RJSONIO","RSQLite",
"stringr","survival", "XML", "xtable",  "yaml"))