tidyexposomics

This is the development version of tidyexposomics; to use it, please install the devel version of Bioconductor.

Integrated Exposure-Omics Analysis Powered by Tidy Principles

Bioconductor version: Development (3.23)

The tidyexposomics package is designed to facilitate the integration of exposure and omics data to identify exposure-omics associations. We structure our commands to fit into the tidyverse framework, where commands are designed to be simplified and intuitive. Here we provide functionality to perform quality control, sample and exposure association analysis, differential abundance analysis, multi-omics integration, and functional enrichment analysis.

Author: Jason Laird [aut, cre] ORCID: 0009-0000-5994-2236 , Thomas Hartung [ctb] ORCID: 0000-0003-1359-7689 , Fenna Sillé [ctb] ORCID: 0000-0003-4305-2049 , Alexandra Maertens [ctb] ORCID: 0000-0002-2077-2011 , JHU Discovery Award [fnd]

Maintainer: Jason Laird <jasonlaird5353 at gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("tidyexposomics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GraphAndNetwork, MultipleComparison, Proteomics, QualityControl, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep
Version	0.99.12
In Bioconductor since	BioC 3.23 (R-4.6)
License	MIT + file LICENSE
Depends	R (>= 4.5.0), MultiAssayExperiment
Imports	BiocFileCache, broom, cluster, dplyr, DT, factoextra, fenr, ggplot2 (>= 3.4.0), ggpubr, ggrepel, Hmisc, httr, igraph, jsonlite, limma, MASS, methods, mixOmics, naniar, purrr, readr, RGCCA, rlang, S4Vectors, scales, shiny, stats, stringr, SummarizedExperiment, tibble, tidybulk, tidyr, utils
System Requirements
URL	https://bionomad.github.io/tidyexposomics/
Bug Reports	https://github.com/BioNomad/tidyexposomics/issues

Suggests	BiocStyle, circlize, curl, densityClust, DiagrammeR, dynamicTreeCut, edgeR, forcats, ggh4x, ggnewscale, ggraph, ggridges, ggsci, ggvenn, grid, gridExtra, impute, janitor, knitr, matrixStats, mice, mirt, missForest, MOFA2, nipalsMCIA, openxlsx, patchwork, reticulate, rmarkdown, testthat (>= 3.0.0), tidygraph, tidyHeatmap, tidytext, tidyverse
Linking To
Enhances
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)	tidyexposomics_0.99.12.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tidyexposomics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tidyexposomics
Bioc Package Browser	https://code.bioconductor.org/browse/tidyexposomics/
Package Short Url	https://bioconductor.org/packages/tidyexposomics/
Package Downloads Report	Download Stats