omicRexposome

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see omicRexposome.

Exposome and omic data associatin and integration analysis


Bioconductor version: 3.9

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: Carles Hernandez-Ferrer <carles.hernandez at isglobal.org>

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

Installation

To install this package, start R (version "3.6") 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

Details

biocViews DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneRegulation, ImmunoOncology, MultipleComparison, Proteomics, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep
Version 1.6.0
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
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Suggests BiocStyle, knitr, rmarkdown, snpStats, brgedata
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Package Archives

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

Source Package omicRexposome_1.6.0.tar.gz
Windows Binary omicRexposome_1.6.0.zip
Mac OS X 10.11 (El Capitan) omicRexposome_1.6.0.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
Old Source Packages for BioC 3.9 Source Archive