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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 (>= 4.6.0) |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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_0.99.4.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/TiDEomics/ |
| Package Short Url | https://bioconductor.org/packages/TiDEomics/ |
| Package Downloads Report | Download Stats |