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ASSIGN

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

Adaptive Signature Selection and InteGratioN (ASSIGN)


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Primer HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, GeneExpression, Pathways, Software
Version 1.39.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License MIT + file LICENSE
Depends R (>= 3.4)
Imports gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml
System Requirements
URL https://compbiomed.github.io/ASSIGN/
Bug Reports https://github.com/compbiomed/ASSIGN/issues
See More
Suggests testthat, BiocStyle, lintr, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me TBSignatureProfiler
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package ASSIGN_1.39.0.tar.gz
Windows Binary ASSIGN_1.39.0.zip
macOS Binary (x86_64) ASSIGN_1.39.0.tgz
macOS Binary (arm64) ASSIGN_1.39.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ASSIGN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ASSIGN
Bioc Package Browser https://code.bioconductor.org/browse/ASSIGN/
Package Short Url https://bioconductor.org/packages/ASSIGN/
Package Downloads Report Download Stats