omicRexposome

Exposome and omic data associatin and integration analysis

Bioconductor version: Release (3.20)

omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

Author: Carles Hernandez-Ferrer [aut, cre], Juan R. González [aut]

Maintainer: Xavier Escribà Montagut <xavier.escriba at isglobal.org>

Citation (from within R, enter citation("omicRexposome")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("omicRexposome")

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("omicRexposome")

Exposome Data Integration with Omic Data	HTML	R Script
Reference Manual	PDF
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneRegulation, ImmunoOncology, MultipleComparison, Proteomics, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep
Version	1.28.0
In Bioconductor since	BioC 3.6 (R-3.4) (7 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), Biobase
Imports	stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, snpStats, brgedata
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	omicRexposome_1.28.0.tar.gz
Windows Binary (x86_64)	omicRexposome_1.28.0.zip
macOS Binary (x86_64)	omicRexposome_1.28.0.tgz
macOS Binary (arm64)	omicRexposome_1.27.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/omicRexposome
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/omicRexposome
Bioc Package Browser	https://code.bioconductor.org/browse/omicRexposome/
Package Short Url	https://bioconductor.org/packages/omicRexposome/
Package Downloads Report	Download Stats