MPAC
This is the development version of MPAC; for the stable release version, see MPAC.
All Bioconductor versions of MPAC
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20
Multi-omic Pathway Analysis of Cells
Bioconductor version: 3.24 · Package version: 1.7.0
Multi-omic Pathway Analysis of Cells (MPAC), integrates multi-omic data for understanding cellular mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.
Author: Peng Liu [aut, cre] 
, Paul Ahlquist [aut], Irene Ong [aut], Anthony Gitter [aut]
Maintainer: Peng Liu <pliu55.wisc+bioconductor at gmail.com>
Citation
From within R, enter citation("MPAC"):
Peng Liu, Paul Ahlquist, Irene Ong, Anthony Gitter. MPAC: Multi-omic Pathway Analysis of Cells. doi:10.18129/B9.bioc.MPAC, R package version 1.7.0, https://bioconductor.org/packages/MPAC.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MPAC")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.7.0 |
| License | GPL-3 |
| URL | https://github.com/pliu55/MPAC |
| Bug Reports | https://github.com/pliu55/MPAC/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| Downloads rank | 2209 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, ImmunoOncology, RNASeq, Sequencing, Software, Survival, Technology |
| Package Short Url | https://bioconductor.org/packages/MPAC/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | MPAC_1.7.0.tar.gz |
| macOS binary (arm64) | MPAC_1.7.0.tgz |
| macOS binary (x86_64) | MPAC_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MPAC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MPAC |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.4.0)
Imports: data.table (>= 1.14.2), SummarizedExperiment (>= 1.30.2), BiocParallel (>= 1.28.3), fitdistrplus (>= 1.1), igraph (>= 1.4.3), BiocSingular (>= 1.10.0), S4Vectors (>= 0.32.3), SingleCellExperiment (>= 1.16.0), bluster (>= 1.4.0), fgsea (>= 1.20.0), scran (>= 1.22.1), ComplexHeatmap (>= 2.16.0), circlize (>= 0.4.16), scales (>= 1.3.0), stringr (>= 1.5.1), viridis (>= 0.6.5), ggplot2 (>= 3.5.1), ggraph (>= 2.2.1), survival (>= 3.7), survminer (>= 0.4.9), grid, stats
Suggests: rmarkdown, knitr, svglite, bookdown (>= 0.34), testthat (>= 3.0.0)