tidyexposomics
Integrated Exposure-Omics Analysis Powered by Tidy Principles
Bioconductor version: 3.24 · Package version: 1.1.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidyexposomics")Details
| Maintainer | Jason Laird <jasonlaird5353@gmail.com> |
| Author | Jason Laird [aut, cre] (ORCID: <https://orcid.org/0009-0000-5994-2236>), Thomas Hartung [ctb] (ORCID: <https://orcid.org/0000-0003-1359-7689>), Fenna Sillé [ctb] (ORCID: <https://orcid.org/0000-0003-4305-2049>), Alexandra Maertens [ctb] (ORCID: <https://orcid.org/0000-0002-2077-2011>), JHU Discovery Award [fnd] |
| License | MIT + file LICENSE |
| URL | https://bionomad.github.io/tidyexposomics/ |
| Bug Reports | https://github.com/BioNomad/tidyexposomics/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GraphAndNetwork, MultipleComparison, Proteomics, QualityControl, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/tidyexposomics/ |
Citation
From within R, enter citation("tidyexposomics"):
Jason Laird. tidyexposomics: Integrated Exposure-Omics Analysis Powered by Tidy Principles. doi:10.18129/B9.bioc.tidyexposomics, R package version 1.1.2, https://bioconductor.org/packages/tidyexposomics.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | tidyexposomics_1.1.2.tar.gz |
| Windows binary (x86_64) | tidyexposomics_1.1.1.zip |
| macOS binary (arm64) | tidyexposomics_1.1.1.tgz |
| macOS binary (x86_64) | tidyexposomics_1.1.2.tgz |
Dependencies
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
Suggests: BiocStyle, circlize, curl, densityClust, DiagrammeR, dynamicTreeCut, edgeR, forcats, ggh4x, ggnewscale, ggraph, ggridges, ggsci, ggvenn, grid, gridExtra, impute, janitor, knitr, Matrix, matrixStats, mice, mirt, missForest, MOFA2, nipalsMCIA, openxlsx, patchwork, reticulate, rmarkdown, testthat (>= 3.0.0), tidygraph, tidyHeatmap, tidytext, tidyverse