Package: tidyexposomics
Title: Integrated Exposure-Omics Analysis Powered by Tidy Principles
Version: 1.1.1
Authors@R: 
    c(
    person(given = "Jason",
    family  = "Laird",
    email = "jasonlaird5353@gmail.com",
    role = c("aut", "cre"),
    comment = c(ORCID = "0009-0000-5994-2236")
    ),
    person(given = "Thomas",
    family  = "Hartung",
    email = "thartun1@jhu.edu",
    role = c("ctb"),
    comment = c(ORCID = "0000-0003-1359-7689")
    ),
    person(given = "Fenna",
    family  = "Sillé",
    email = "fsille1@jhu.edu",
    role = c("ctb"),
    comment = c(ORCID = "0000-0003-4305-2049")
    ),
    person(given = "Alexandra",
    family  = "Maertens",
    email = "amaerte1@jhu.edu",
    role = c("ctb"),
    comment = c(ORCID = "0000-0002-2077-2011")
    ),
    person("JHU Discovery Award", role = "fnd")
    )
Description: 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.
License: MIT + file LICENSE
URL: https://bionomad.github.io/tidyexposomics/
BugReports: https://github.com/BioNomad/tidyexposomics/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
biocViews: Software, Transcriptomics, GeneExpression, Epigenetics,
        Proteomics, DifferentialExpression, DifferentialMethylation,
        QualityControl, GraphAndNetwork, MultipleComparison,
        Regression, StatisticalMethod, Visualization, WorkflowStep
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
Depends: R (>= 4.5.0), MultiAssayExperiment
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
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev
        make texlive libicu-dev libjpeg-dev libpng-dev libuv1-dev
        libxml2-dev libgl1-mesa-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-04 21:08:39 UTC
RemoteUrl: https://github.com/bioc/tidyexposomics
RemoteRef: HEAD
RemoteSha: 4725f84037ccdb5b1652a3e4d7043d01eaaa19d4
NeedsCompilation: no
Packaged: 2026-07-05 06:44:14 UTC; root
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]
Maintainer: Jason Laird <jasonlaird5353@gmail.com>