Package: TiDEomics
Title: Time-course Differential Expression analysis of omics data
Version: 0.99.6
Date: 2026-10-27
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 an integrated workflow for multi-group
        time-course omics data analysis. It uses model-based
        differential expression, variance decomposition, and
        co-expression module analysis with WGCNA to characterise
        temporal, group, and group-specific temporal effects.
        Multi-dataset and multi-omics comparisons and consensus module
        identification can be performed using shared features. The
        package includes quality control, data processing, functional
        enrichment, and integrated visualisation. It supports data with
        missing values, and operates on SummarizedExperiment objects
        for interoperability with the Bioconductor ecosystem.
License: GPL (>= 2)
URL: https://bioconductor.org/packages/TiDEomics/,
        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, 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: 8.1.1
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: 2026-10-27 20:21:36 UTC
RemoteUrl: https://github.com/bioc/TiDEomics
RemoteRef: HEAD
RemoteSha: 5a15b0c166428d09c651cb05ae26a90fa50bc66c
NeedsCompilation: no
Packaged: 2026-10-28 00:15:54 UTC; root
Author: Tianen He [aut, cre] (ORCID: <https://orcid.org/0000-0001-6864-0723>)
Maintainer: Tianen He <tianen.he@ndm.ox.ac.uk>