TiDEomics
This is the development version of TiDEomics; to use it, please install the devel version of Bioconductor.
Time-course Differential Expression analysis of omics data
Bioconductor version: 3.24 · Package version: 0.99.5
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.
Maintainer: Tianen He <tianen.he at ndm.ox.ac.uk>
Citation
From within R, enter citation("TiDEomics"):
Tianen He. TiDEomics: Time-course Differential Expression analysis of omics data. doi:10.18129/B9.bioc.TiDEomics, R package version 0.99.5, https://bioconductor.org/packages/TiDEomics.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("TiDEomics")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.5 |
| License | GPL (>= 2) |
| URL | https://github.com/hte123/TiDEomics https://hte123.github.io/TiDEomics |
| Bug Reports | https://github.com/hte123/TiDEomics/issues |
| Last updated | 2026-07-31 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2373 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, MassSpectrometry, MultipleComparison, Pathways, Proteomics, QualityControl, Software, TimeCourse, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/TiDEomics/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TiDEomics")| TiDEomics Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | TiDEomics_0.99.5.tar.gz |
| Windows binary (x86_64) | TiDEomics_0.99.5.zip |
| macOS binary (arm64) | TiDEomics_0.99.5.tgz |
| macOS binary (x86_64) | TiDEomics_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TiDEomics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TiDEomics |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
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
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.1.0), plotly, enrichR, org.Hs.eg.db, org.Mm.eg.db, msigdbr, DeeDeeExperiment