tidyexposomics
Integrated Exposure-Omics Analysis Powered by Tidy Principles
Bioconductor version: 3.23 · Package version: 1.0.0
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 |
| Downloads rank | 77 |
| Source branch | RELEASE_3_23 |
| biocViews | DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GraphAndNetwork, MultipleComparison, Proteomics, QualityControl, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep |
Documentation
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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, matrixStats, mice, mirt, missForest, MOFA2, nipalsMCIA, openxlsx, patchwork, reticulate, rmarkdown, testthat (>= 3.0.0), tidygraph, tidyHeatmap, tidytext, tidyverse