MPAC: inferring pathway activities from multi-omic data

Introduction
Installation
Shiny App
Software Dependency
Reference
Contact
License

Introduction

Multi-omic Pathway Analysis of Cells (MPAC) is an R package that interprets multi-omic data through the prior knowledge of biological pathways. The workflow of MPAC contains several steps, which are shown in the figure below. MPAC has a vignette that describes each function in details.

Installation

From GitHub

Start R and enter:

devtools::install_github('pliu55/MPAC')

From Bioconductor

Start R and enter:

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

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

BiocManager::install("MPAC")

Shiny App

To explore key results reported in the MPAC manuscript as well as associated results please check out this R Shiny app.

Software Dependency

The runPrd() function requires an external software named PARADIGM, which is only available for Linux and MacOS. For details, please see the Required external software section in vignette’s Run PARADIGM: runPrd().

Reference

Manuscript

MPAC: a computational framework for inferring cancer pathway activities from multi-omic data. Peng Liu, David Page, Paul Ahlquist, Irene M. Ong*, Anthony Gitter*. Bioinformatics, Volume 41, Issue 10, October 2025, btaf490, https://doi.org/10.1093/bioinformatics/btaf490, *co-corresponding author