padma

DOI: 10.18129/B9.bioc.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 (3.13)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews BioCarta, GeneExpression, MethylSeq, Pathways, PrincipalComponent, RNASeq, Software, StatisticalMethod
Version 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL (>=3)
Depends R (>= 4.0.0), 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_1.1.0.tar.gz
Windows Binary padma_1.1.0.zip
macOS 10.13 (High Sierra) padma_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/padma
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/padma
Package Short Url https://bioconductor.org/packages/padma/
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