To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ASSIGN")

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

ASSIGN

 

   

This is the development version of ASSIGN; for the stable release version, see ASSIGN.

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor version: Development (3.5)

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, W. Evan Johnson, and Mumtehena Rahman

Maintainer: Ying Shen <yshen3 at bu.edu>, W. Evan Johnson <wej at bu.edu>, David Jenkins <dfj at bu.edu>, Mumtehena Rahman <moom.rahman at utah.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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
Text   LICENSE

Details

biocViews Bayesian, GeneExpression, Pathways, Software
Version 1.11.2
In Bioconductor since BioC 2.14 (R-3.1) (2.5 years)
License MIT + file LICENSE
Depends R (>= 3.2)
Imports gplots, graphics, grDevices, msm, Rlab, stats, sva, utils
LinkingTo
Suggests testthat, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ASSIGN_1.11.2.tar.gz
Windows Binary ASSIGN_1.11.2.zip
Mac OS X 10.9 (Mavericks) ASSIGN_1.11.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ASSIGN
Package Short Url http://bioconductor.org/packages/ASSIGN/
Package Downloads Report Download Stats

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