VIPER R-System Package

Read vignette about VIPER

Download VIPER

Click here to download VIPER version 0.99.0

Installation

In order to install the viper package, the user needs to first install R (http://www.r-project.org) and the mixtools package from Bioconductor (http://www.bioconductor.org).

Once R is installed, mixtools can be easily installed from the R terminal by:

> source("http://bioconductor.org/biocLite.R")
> biocLite("mixtools")

Then, install bcellViper and viper packages from the R terminal by,

> install.packages(c("BcellViper_0.99.0.tar.gz", "Viper_0.99.0.tar.gz"), repos = NULL)

or from the system prompt by,

R CMD INSTALL BcellViper_0.99.0.tar.gz
R CMD INSTALL Viper_0.99.0.tar.gz

bcellViper data package

The bcellViper data package is required to run the examples in the documentation and vignette of the viper package. Please install this package before installing viper.

bcellViper v0.99.0

Additional regulatory networks

Human B-cell transcriptional regulatory network based on Affymetrix U95Av2 platform

Human B-cell transcriptional regulatory network based on Affymetrix U133plus2 platform

Human glioma transcriptional regulatory network

MCF7 human breast carcinoma cell line transcriptional regulatory network

Human breast carcinoma signalome regulatory network

Reference

Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet. 2016 Jun 20. [Epub ahead of print]