MPAC

An R package to infer cancer pathway activities from multi-omic data

https://github.com/pliu55/mpac

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 7 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

An R package to infer cancer pathway activities from multi-omic data

Basic Info

Host: GitHub
Owner: pliu55
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://bioconductor.org/packages/MPAC/
Size: 676 KB

Statistics

Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 3

Created almost 3 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License

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:

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.

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. 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.

Owner

Name: Peng Liu
Login: pliu55
Kind: user
Company: UW-Madison

Website: https://www.ncbi.nlm.nih.gov/myncbi/peng.liu.7/bibliography/public/
Repositories: 3
Profile: https://github.com/pliu55

GitHub Events

Total

Release event: 1
Push event: 39
Create event: 2

Last Year

Release event: 1
Push event: 39
Create event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 0
Total pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 10 days
Total issue authors: 0
Total pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Packages

Total packages: 1
Total downloads:
- bioconductor 2,337 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 2
Total maintainers: 1

bioconductor.org: MPAC

Multi-omic Pathway Analysis of Cells

Homepage: https://github.com/pliu55/MPAC
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/MPAC/inst/doc/MPAC.pdf
License: GPL-3
Latest release: 1.2.0
published about 1 year ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 2,337 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 31.5%

Average: 42.2%

Downloads: 95.0%

Maintainers (1)

pliu55.wisc+bioconductor@gmail.com