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 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.
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 |
| TiDEomics Tutorial: Multi-Dataset/Multi-Omics Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, MultipleComparison, Pathways, Proteomics, QualityControl, Software, TimeCourse, Transcriptomics, Visualization |
| Version | 0.99.7 |
| 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://bioconductor.org/packages/TiDEomics/ 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_0.99.7.tar.gz |
| Windows Binary (x86_64) | TiDEomics_0.99.5.zip |
| macOS Binary (big-sur-x86_64) | TiDEomics_0.99.6.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 |