ASSIGN is an R package for adaptive profiling of genomic signatures
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README.md

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 literatures 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:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ASSIGN")

Or install the development version from github:

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