ASSIGN

DOI: 10.18129/B9.bioc.ASSIGN    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ASSIGN.

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor version: 3.7

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 literature 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>

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")

 

HTML	R Script	Primer
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Bayesian, GeneExpression, Pathways, Software
Version	1.16.0
In Bioconductor since	BioC 2.14 (R-3.1) (4.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.4)
Imports	gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ASSIGN_1.16.0.tar.gz
Windows Binary	ASSIGN_1.16.0.zip
Mac OS X 10.11 (El Capitan)	ASSIGN_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ASSIGN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ASSIGN
Package Short Url	http://bioconductor.org/packages/ASSIGN/
Package Downloads Report	Download Stats