Package: TiDEomics
Title: Time-course Differential Expression analysis of omics data
Version: 0.99.4
Date: 2026-07-24
Authors@R: 
    person("Tianen", "He",
            email = "tianen.he@ndm.ox.ac.uk",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6864-0723"))
Description: TiDEomics provides a comprehensive workflow for multi-group
    time-course omics data analysis, analysing time-dominant, group-dominant,
    and group-specific temporal effects through pairwise differential
    expression, variance decomposition, and co-expression module analysis
    (WGCNA). The package integrates quality control, data processing,
    functional enrichment, and extensive visualisation. It supports datasets
    with missing values (e.g., mass spectrometry-based proteomics), and
    operates on SummarizedExperiment objects to ensure compatibility with
    the Bioconductor ecosystem.
License: GPL (>= 2)
URL: https://github.com/hte123/TiDEomics,
        https://hte123.github.io/TiDEomics
BugReports: https://github.com/hte123/TiDEomics/issues
biocViews: Software, GeneExpression, DifferentialExpression,
        Proteomics, Transcriptomics, TimeCourse, MultipleComparison,
        Pathways, Visualization, MassSpectrometry, QualityControl
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Imports: circlize, clusterProfiler, ComplexHeatmap, dplyr, enrichplot,
        ggforce, ggh4x, ggplot2, ggplotify, ggpubr, ggrepel, ggridges,
        ggsci, limma, lme4, methods, patchwork, pbapply, PCAtools,
        randtests, scales, SummarizedExperiment, tibble, tidyr, Trendy,
        umap, WGCNA
Depends: R (>= 4.6.0)
LazyData: false
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.1.0), plotly,
        enrichR, org.Hs.eg.db, org.Mm.eg.db, msigdbr, DeeDeeExperiment
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
git_url: https://git.bioconductor.org/packages/TiDEomics
git_branch: devel
git_last_commit: 345c8ad
git_last_commit_date: 2026-07-24
Repository: Bioconductor 3.24
Date/Publication: 2026-07-27
NeedsCompilation: no
Packaged: 2026-07-28 00:42:01 UTC; biocbuild
Author: Tianen He [aut, cre] (ORCID: <https://orcid.org/0000-0001-6864-0723>)
Maintainer: Tianen He <tianen.he@ndm.ox.ac.uk>
