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: Development (3.24)
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("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.
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 |
Details
| biocViews | DifferentialExpression, GeneExpression, MassSpectrometry, MultipleComparison, Pathways, Proteomics, QualityControl, Software, TimeCourse, Transcriptomics, Visualization |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 2) |
| 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 |
| System Requirements | |
| URL | https://github.com/hte123/TiDEomics https://hte123.github.io/TiDEomics |
| Bug Reports | https://github.com/hte123/TiDEomics/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.1.0), plotly, enrichR, org.Hs.eg.db, org.Mm.eg.db, msigdbr, DeeDeeExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (64-bit only) |
| macOS Binary (big-sur-x86_64) | TiDEomics_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | 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 Short Url | https://bioconductor.org/packages/TiDEomics/ |
| Package Downloads Report | Download Stats |