ASSIGN

DOI: 10.18129/B9.bioc.ASSIGN    

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor version: Release (3.11)

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 (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ASSIGN")

For older versions of R, please refer to the appropriate Bioconductor release.

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		NEWS
Text		LICENSE

Details

biocViews	Bayesian, GeneExpression, Pathways, Software
Version	1.24.0
In Bioconductor since	BioC 2.14 (R-3.1) (6.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.4)
Imports	gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml
LinkingTo
Suggests	testthat, BiocStyle, lintr, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://compbiomed.github.io/ASSIGN/
BugReports	https://github.com/compbiomed/ASSIGN/issues
Depends On Me
Imports Me	TBSignatureProfiler
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ASSIGN_1.24.0.tar.gz
Windows Binary	ASSIGN_1.24.0.zip
macOS 10.13 (High Sierra)	ASSIGN_1.24.0.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	https://bioconductor.org/packages/ASSIGN/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive