Package: MPAC
Title: Multi-omic Pathway Analysis of Cells
Version: 1.7.0
Authors@R: c(
    person(given="Peng", family="Liu", 
           email="pliu55.wisc+bioconductor@gmail.com", 
           role = c("aut", "cre"), comment=c(ORCID="0000-0001-5655-2259")),
    person(given="Paul",    family="Ahlquist", role = c("aut")),
    person(given="Irene",   family="Ong",      role = c("aut")),
    person(given="Anthony", family="Gitter",   role = c("aut")))
Description: 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.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0)
URL: https://github.com/pliu55/MPAC
BugReports: https://github.com/pliu55/MPAC/issues
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)
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: Software, Technology, Sequencing, RNASeq, Survival,
        Clustering, ImmunoOncology
SystemsRequirements: The `runPrd()` function requires an external
        software named PARADIGM. For details, please see the 'Required
        external software' section in vignette's 'Run PARADIGM:
        runPrd()'.
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libjpeg-dev libpng-dev libxml2-dev
        libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:03:14 UTC
RemoteUrl: https://github.com/bioc/MPAC
RemoteRef: HEAD
RemoteSha: e25384ace4c3ccbc05bdf83260fd4dc38695d47f
NeedsCompilation: no
Packaged: 2026-07-04 01:54:01 UTC; root
Author: Peng Liu [aut, cre] (ORCID: <https://orcid.org/0000-0001-5655-2259>),
  Paul Ahlquist [aut],
  Irene Ong [aut],
  Anthony Gitter [aut]
Maintainer: Peng Liu <pliu55.wisc+bioconductor@gmail.com>