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"))