MPAC
Multi-omic Pathway Analysis of Cells
Bioconductor version: 3.23 · Package version: 1.6.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MPAC")Details
| Maintainer | Peng Liu <pliu55.wisc+bioconductor@gmail.com> |
| Author | Peng Liu [aut, cre] (ORCID: <https://orcid.org/0000-0001-5655-2259>), Paul Ahlquist [aut], Irene Ong [aut], Anthony Gitter [aut] |
| License | GPL-3 |
| URL | https://github.com/pliu55/MPAC |
| Bug Reports | https://github.com/pliu55/MPAC/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, ImmunoOncology, RNASeq, Sequencing, Software, Survival, Technology |
| Package Short Url | https://bioconductor.org/packages/MPAC/ |
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 1.6.0, https://bioconductor.org/packages/MPAC.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | MPAC_1.6.0.tar.gz |
| Windows binary (x86_64) | MPAC_1.5.0.zip |
| macOS binary (arm64) | MPAC_1.6.0.tgz |
| macOS binary (x86_64) | MPAC_1.6.0.tgz |
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)