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# ASSIGN: Adaptive Signature Selection and InteGratioN

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

__Maintainer__: [David Jenkins](https://github.com/dfjenkins3), [W. Evan Johnson](https://github.com/wevanjohnson/), [Mumtehena Rahman](https://github.com/mumtahena), 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:

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

Or install the development version from github:

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