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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "MPAC" in publications use:'
type: software
license: GPL-3.0-only
title: 'MPAC: Multi-omic Pathway Analysis of Cells'
version: 1.6.0
doi: 10.1093/bioinformatics/btaf490
identifiers:
- type: doi
  value: 10.32614/CRAN.package.MPAC
abstract: 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.
authors:
- family-names: Liu
  given-names: Peng
  email: pliu55.wisc+bioconductor@gmail.com
  orcid: https://orcid.org/0000-0001-5655-2259
- family-names: Ahlquist
  given-names: Paul
- family-names: Ong
  given-names: Irene
- family-names: Gitter
  given-names: Anthony
preferred-citation:
  type: article
  title: 'MPAC: a computational framework for inferring cancer pathway activities
    from multi-omic data'
  authors:
  - family-names: Liu
    given-names: Peng
    email: pliu55.wisc+bioconductor@gmail.com
    orcid: https://orcid.org/0000-0001-5655-2259
  - family-names: Page
    given-names: David
  - family-names: Ahlquist
    given-names: Paul
  - family-names: Ong
    given-names: Irene M.
  - family-names: Gitter
    given-names: Anthony
  year: '2025'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/btaf490
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/pliu55/MPAC
commit: 2a03ee8ae4e5c025df361f723ae02a7b0d61f03e
url: https://github.com/pliu55/MPAC
date-released: '2026-04-28'
contact:
- family-names: Liu
  given-names: Peng
  email: pliu55.wisc+bioconductor@gmail.com
  orcid: https://orcid.org/0000-0001-5655-2259