Package: padma
Type: Package
Title: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Version: 1.21.0
Authors@R: c(
  person(given="Andrea", 
         family="Rau", 
         email="andrea.rau@inrae.fr", 
         role=c("cre", "aut"), 
         comment = c(ORCID = "0000-0001-6469-488X")),
  person(given="Regina",
         family="Manansala",
         email="manansa2@uwm.edu",
         role="aut"),
  person(given="Florence",
         family="Jaffrézic",
         email="florence.jaffrezic@inrae.fr",
         role="ctb"),
  person(given="Denis",
         family="Laloë",
         email="denis.laloe@inrae.fr",
         role="aut"),
  person(given="Paul",
         family="Auer",
         email="pauer@uwm.edu",
         role="aut"))
Depends: 
  R (>= 4.1.0), 
  SummarizedExperiment, 
  S4Vectors
Imports: 
  FactoMineR, 
  MultiAssayExperiment,
  methods,
  graphics,
  stats,
  utils
Suggests:
  testthat, 
  BiocStyle, 
  knitr, 
  rmarkdown, 
  KEGGREST, 
  missMDA, 
  ggplot2, 
  ggrepel, 
  car, 
  cowplot,
  reshape2
Description: 
  Use multiple factor analysis to calculate individualized pathway-centric 
  scores of deviation with respect to the sampled population based on multi-omic 
  assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical 
  and numerical outputs are provided to identify highly aberrant individuals 
  for a particular pathway of interest, as well as the gene and omics drivers of 
  aberrant multi-omic profiles.
License: GPL (>=3)
URL: https://github.com/andreamrau/padma
https: //github.com/andreamrau/padma/issues
biocViews: 
  Software,
  StatisticalMethod,
  PrincipalComponent,
  GeneExpression,
  Pathways,
  RNASeq,
  BioCarta,
  MethylSeq
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 7.3.1
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/padma
git_branch: devel
git_last_commit: 79cd1b2
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
