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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

MaintainerJason Laird <jasonlaird5353@gmail.com>
AuthorJason 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]
LicenseMIT + file LICENSE
URLhttps://bionomad.github.io/tidyexposomics/
Bug Reportshttps://github.com/BioNomad/tidyexposomics/issues
Downloads rank77
Source branchRELEASE_3_23
biocViewsDifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GraphAndNetwork, MultipleComparison, Proteomics, QualityControl, Regression, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep

Documentation

Download

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