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Bioconductor - MPAC (development version)

MPAC

This is the development version of MPAC; for the stable release version, see MPAC.

Multi-omic Pathway Analysis of Cells

Bioconductor version: Development (3.22)

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] ORCID: 0000-0001-5655-2259 , 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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MPAC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MPAC")
Details biocViews Clustering, ImmunoOncology, RNASeq, Sequencing, Software, Survival, Technology Version 1.3.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License GPL-3 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 System Requirements URL https://github.com/pliu55/MPAC Bug Reports https://github.com/pliu55/MPAC/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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