To install this package, start R and enter:

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

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

ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor version: 3.0

ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.

Author: Ying Shen, Andrea H. Bild, and W. Evan Johnson

Maintainer: Ying Shen <yshen3 at bu.edu>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("ASSIGN")

 

PDF R Script Primer
PDF   Reference Manual

Details

biocViews Bayesian, GeneExpression, Pathways, Software
Version 1.2.0
In Bioconductor since BioC 2.14 (R-3.1)
License MIT
Depends Rlab, msm, gplots
Imports graphics, grDevices, stats, utils
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Enhances
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Depends On Me
Imports Me
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Build Report  

Package Archives

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

Package Source ASSIGN_1.2.0.tar.gz
Windows Binary ASSIGN_1.2.0.zip
Mac OS X 10.6 (Snow Leopard) ASSIGN_1.2.0.tgz
Mac OS X 10.9 (Mavericks) ASSIGN_1.2.0.tgz
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