padma

DOI: 10.18129/B9.bioc.padma  

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	BioCarta, GeneExpression, MethylSeq, Pathways, PrincipalComponent, RNASeq, Software, StatisticalMethod
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL (>=3)
Depends	R (>= 4.1.0), SummarizedExperiment, S4Vectors
Imports	FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot
SystemRequirements
Enhances
URL	https://github.com/andreamrau/padma
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	padma_1.8.0.tar.gz
Windows Binary	padma_1.8.0.zip
macOS Binary (x86_64)	padma_1.8.0.tgz
macOS Binary (arm64)	padma_1.8.0.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