ExpoRiskR
This is the released version of ExpoRiskR; for the devel version, see ExpoRiskR.
Exposure-Aware Multi-Omics Risk Modeling
Bioconductor version: Release (3.23)
ExpoRiskR provides tools for exposure-aware multi-omics risk modeling in translational and environmental health studies. The package aligns sample identifiers across exposure and multi-omics blocks, performs lightweight preprocessing, and fits exposure-adjusted association models to build interpretable microbe–metabolite networks. It also computes simple exposure perturbation summaries and generates publication-ready visualizations. Workflows support both matrix-based inputs and SummarizedExperiment objects.
Author: Prem Prashant Chaudhary [aut, cre]
Maintainer: Prem Prashant Chaudhary <chaudharyp2 at nih.gov>
citation("ExpoRiskR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ExpoRiskR")
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("ExpoRiskR")| ExpoRiskR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Metabolomics, Microbiome, Network, Regression, Software, SystemsBiology |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | stats, ggplot2, igraph, SummarizedExperiment, S4Vectors, utils |
| System Requirements | |
| URL | https://github.com/ppchaudhary/ExpoRiskR |
| Bug Reports | https://github.com/ppchaudhary/ExpoRiskR/issues |
See More
| Suggests | BiocStyle, BiocCheck, knitr, rmarkdown, withr, testthat (>= 3.0.0) |
| 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 | ExpoRiskR_1.0.0.tar.gz |
| Windows Binary (x86_64) | ExpoRiskR_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | ExpoRiskR_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | ExpoRiskR_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ExpoRiskR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ExpoRiskR |
| Bioc Package Browser | https://code.bioconductor.org/browse/ExpoRiskR/ |
| Package Short Url | https://bioconductor.org/packages/ExpoRiskR/ |
| Package Downloads Report | Download Stats |