omicRexposome
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see omicRexposome.
Exposome and omic data associatin and integration analysis
Bioconductor version: 3.16
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("omicRexposome")):
Installation
To install this package, start R (version "4.2") 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 | ||
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneRegulation, ImmunoOncology, MultipleComparison, Proteomics, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, snpStats, brgedata |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | omicRexposome_1.20.0.tar.gz |
| Windows Binary | omicRexposome_1.20.0.zip |
| macOS Binary (x86_64) | omicRexposome_1.20.0.tgz |
| macOS Binary (arm64) | omicRexposome_1.20.0.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 3.16 | Source Archive |