inst/staticdocs/INSTALLATIONs_tmp.md

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

1. R requirement

R (http://www.r-project.org) is a language and environment for statistical computing and graphics. We assume R (version 3.1.0) has been installed in your local machine. It can be installed following quick instructions below for different platforms (Windows, Mac, and Linux).

• Quick link for Windows: Download R for Windows.

• Quick link for Mac: Download R for Mac OS X 10.6 (Snow Leopard or higher).

• Below are shell command lines in Terminal (for Linux):

Assume you have a ROOT (sudo) privilege:

sudo su
wget http://www.stats.bris.ac.uk/R/src/base/R-3/R-3.1.0.tar.gz
tar xvfz R-3.1.0.tar.gz
cd R-3.1.0
./configure
make
make check
make install
R # start R

Assume you do not have a ROOT privilege and want R installation under your home directory (below /home/hfang should be replaced with yours):

wget http://www.stats.bris.ac.uk/R/src/base/R-3/R-3.1.0.tar.gz
tar xvfz R-3.1.0.tar.gz
cd R-3.1.0
./configure --prefix=/home/hfang/R-3.1.0
make
make check
make install
/home/hfang/R-3.1.0/bin/R # start R

2. Installation of the package

Notes: below are R command lines (NOT shell command lines in Terminal).

First, install dependant/imported/suggested packages:

source("http://bioconductor.org/biocLite.R")
for(pkg in c("hexbin","ape","supraHex","graph","Rgraphviz","igraph","Biobase","limma","survival")){
    if(!require(pkg, character.only=T)) biocLite(pkg)
}

Second, install the package dnet under stable release version:

install.packages("dnet",repos="http://cran.r-project.org",type="source")

Notes: to install the package dnet under latest development version, please run:

install.packages(pkgs=c("dnet","supraHex"),repos="http://R-Forge.R-project.org", type="source")

3. Workflow of the package

It provides a brief overview of how the package operates and what you expect to get from it.

dnet documentation built on Feb. 20, 2020, 5:08 p.m.