tidyexposomics
This is the released version of tidyexposomics; for the devel version, see tidyexposomics.
Integrated Exposure-Omics Analysis Powered by Tidy Principles
Bioconductor version: Release (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] 
, Thomas Hartung [ctb] , Fenna Sillé [ctb] , Alexandra Maertens [ctb] , JHU Discovery Award [fnd]
Maintainer: Jason Laird <jasonlaird5353 at gmail.com>
citation("tidyexposomics")):Jason Laird. tidyexposomics: Integrated Exposure-Omics Analysis Powered by Tidy Principles. doi:10.18129/B9.bioc.tidyexposomics, R package version 1.0.0, https://bioconductor.org/packages/tidyexposomics.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidyexposomics")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("tidyexposomics")| tidyexposomics: Custom Analysis | HTML | R Script |
| tidyexposomics: Exposure Scores | HTML | R Script |
| tidyexposomics: Exposure Annotation | HTML | R Script |
| tidyexposomics: integrated exposure-omics analysis powered by tidy principles | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GraphAndNetwork, MultipleComparison, Proteomics, QualityControl, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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 |
See More
| 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 | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidyexposomics_1.0.0.tar.gz |
| Windows Binary (x86_64) | tidyexposomics_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | tidyexposomics_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | tidyexposomics_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidyexposomics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidyexposomics |
| Package Short Url | https://bioconductor.org/packages/tidyexposomics/ |
| Package Downloads Report | Download Stats |