ASSIGN

DOI: 10.18129/B9.bioc.ASSIGN    

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor version: Release (3.8)

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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ASSIGN", version = "3.8")

Documentation

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

browseVignettes("ASSIGN")

 

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Details

biocViews Bayesian, GeneExpression, Pathways, Software
Version 1.18.0
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, yaml
LinkingTo
Suggests testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL https://compbiomed.github.io/ASSIGN/
BugReports https://github.com/compbiomed/ASSIGN/issues
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_1.18.0.tar.gz
Windows Binary ASSIGN_1.18.0.zip
Mac OS X 10.11 (El Capitan) ASSIGN_1.18.0.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

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