padma

DOI:10.18129/B9.bioc.padma

This is thedevelopmentversion of padma; for the stable release version, seepadma.

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Bioconductor version: Development (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

Installation

To install this package, start R (version "4.2") 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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.7.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 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

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	padma_1.7.0.tar.gz
Windows Binary	padma_1.7.0.zip
macOS 10.13 (High Sierra)	padma_1.7.0.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	//www.andersvercelli.com/packages/padma/
Package Downloads Report	Download Stats