ASSIGN: Adaptive Signature Selection and InteGratioN

Author: Ying Shen, Andrea H. Bild, David Jenkins, and W. Evan Johnson

Maintainer: David Jenkins, W. Evan Johnson, Mumtehena Rahman, and Ying Shen yshen3@bu.edu

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.

Installation

ASSIGN is available on Bioconductor:

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

Or install the development version from github:

# install.packages("devtools")
devtools::install_github("compbiomed/ASSIGN")