DOI: 10.18129/B9.bioc.padma  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see padma.

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Bioconductor version: 3.17

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.

Author: Andrea Rau [cre, aut] , Regina Manansala [aut], Florence Jaffrézic [ctb], Denis Laloë [aut], Paul Auer [aut]

Maintainer: Andrea Rau <andrea.rau at>

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biocViews BioCarta, GeneExpression, MethylSeq, Pathways, PrincipalComponent, RNASeq, Software, StatisticalMethod
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL (>=3)
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
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