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padma

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 (3.20)

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("padma")

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

Documentation

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

browseVignettes("padma")
padma package:Quick-start guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BioCarta, GeneExpression, MethylSeq, Pathways, PrincipalComponent, RNASeq, Software, StatisticalMethod
Version 1.15.1
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
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package padma_1.15.1.tar.gz
Windows Binary padma_1.15.0.zip
macOS Binary (x86_64) padma_1.15.1.tgz
macOS Binary (arm64) padma_1.15.0.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/
Package Downloads Report Download Stats