To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

pathifier

Quantify deregulation of pathways in cancer

Bioconductor version: Release (3.0)

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

Author: Yotam Drier

Maintainer: Assif Yitzhaky <assif.yitzhaky at weizmann.ac.il>

Citation (from within R, enter citation("pathifier")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pathifier")

 

PDF R Script Quantify deregulation of pathways in cancer
PDF   Reference Manual

Details

biocViews Network, Software
Version 1.4.0
In Bioconductor since BioC 2.13 (R-3.0)
License Artistic-1.0
Depends
Imports R.oo, princurve
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source pathifier_1.4.0.tar.gz
Windows Binary pathifier_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) pathifier_1.4.0.tgz
Mac OS X 10.9 (Mavericks) pathifier_1.4.0.tgz
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