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

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Bioconductor version: Development (3.19)

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 inrae.fr>

Citation (from within R, enter citation("padma")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

padma package:Quick-start guide HTML R Script
Reference Manual PDF


biocViews BioCarta, GeneExpression, MethylSeq, Pathways, PrincipalComponent, RNASeq, Software, StatisticalMethod
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL (>=3)
Depends R (>= 4.1.0), SummarizedExperiment, S4Vectors
Imports FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils
System Requirements
URL https://github.com/andreamrau/padma
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Suggests testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot
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Follow Installation instructions to use this package in your R session.

Source Package padma_1.13.0.tar.gz
Windows Binary padma_1.13.0.zip
macOS Binary (x86_64) padma_1.13.0.tgz
macOS Binary (arm64) padma_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/padma
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/padma
Bioc Package Browser https://code.bioconductor.org/browse/padma/
Package Short Url https://bioconductor.org/packages/padma/
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