GitHub - pliu55/MPAC: An R package to infer cancer pathway activities from multi-omic data (original) (raw)
MPAC: inferring pathway activities from multi-omic data
Table of Contents
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 avignette 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 outthis R Shiny app.
Software Dependency
The runPrd() function requires an external software namedPARADIGM, which is only available forLinux andMacOS. 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. bioRxiv, 2024.06.15.599113. doi: https://doi.org/10.1101/2024.06.15.599113
Contact
Got a question? Please report it at the issues tab in this repository.
License
MPAC is licensed under the GNU General Public License v3.