Bioconductor Code: MPAC (original) (raw)

[![bioc](http://www.bioconductor.org/shields/years-in-bioc/MPAC.svg)\](http://bioconductor.org/packages/MPAC) [![DOI](https://zenodo.org/badge/664257440.svg)\](https://zenodo.org/doi/10.5281/zenodo.10805479) MPAC: inferring pathway activities from multi-omic data =========================================== * * * Table of Contents ----------------- * [Introduction](#introduction) * [Installation](#installation) * [Shiny App](#shinyapp) * [Software Dependency](#softwaredependency) * [Reference](#reference) * [Contact](#contact) * [License](#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](https://bioconductor.org/packages/devel/bioc/vignettes/MPAC/inst/doc/MPAC.html) that describes each function in details.

## Installation ### From GitHub Start __R__ and enter: ```r devtools::install_github('pliu55/MPAC') ``` ### From Bioconductor Start __R__ and enter: ```r 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](https://github.com/pliu55/MPAC\_Shiny). ## Software Dependency The `runPrd()` function requires an external software named [PARADIGM](https://doi.org/10.1093/bioinformatics/btq182), which is only available for [Linux]( https://github.com/sng87/paradigm-scripts/tree/master/public/exe/LINUX) and [MacOS]( https://github.com/sng87/paradigm-scripts/tree/master/public/exe/MACOSX). 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\](https://doi.org/10.1101/2024.06.15.599113) ## Contact Got a question? Please report it at the [issues tab](https://github.com/pliu55/MPAC/issues) in this repository. ## License MPAC is licensed under the [GNU General Public License v3](LICENSE.md).