omicRexposome

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see omicRexposome.

Exposome and omic data associatin and integration analysis

Bioconductor version: 3.12

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 "4.0") 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 1.12.1

In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)

License MIT + file LICENSE

Depends R (>= 3.4), 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

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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_1.12.1.tar.gz

Windows Binary omicRexposome_1.12.1.zip

macOS 10.13 (High Sierra) omicRexposome_1.12.1.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

Old Source Packages for BioC 3.12 Source Archive