padma
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Bioconductor version: Release (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("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 | 1.16.0 |
| 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 | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | padma_1.16.0.tar.gz |
| Windows Binary (x86_64) | padma_1.16.0.zip |
| macOS Binary (x86_64) | padma_1.16.0.tgz |
| macOS Binary (arm64) | padma_1.16.0.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 |