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 (>= 4.5.0)
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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev perl python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-24 17:45:56 UTC
RemoteUrl: https://github.com/bioc/TiDEomics
RemoteRef: HEAD
RemoteSha: 345c8add43d6ebb7cb7b62ea244d4bfce0d8ff13
NeedsCompilation: no
Packaged: 2026-07-29 21:48:00 UTC; root
Author: Tianen He [aut, cre] (ORCID: <https://orcid.org/0000-0001-6864-0723>)
Maintainer: Tianen He <tianen.he@ndm.ox.ac.uk>
Built: R 4.6.1; ; 2026-07-29 21:51:51 UTC; windows
