padma
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Bioconductor version: Release (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("padma")
):
Installation
To install this package, start R (version "4.4") 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")
padma package:Quick-start guide | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | BioCarta, GeneExpression, MethylSeq, Pathways, PrincipalComponent, RNASeq, Software, StatisticalMethod |
Version | 1.14.1 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 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 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | padma_1.14.1.tar.gz |
Windows Binary | padma_1.14.1.zip |
macOS Binary (x86_64) | padma_1.14.1.tgz |
macOS Binary (arm64) | padma_1.14.1.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 |
Old Source Packages for BioC 3.19 | Source Archive |