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")):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, 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://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 |
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| Enhances | |
| Depends On Me | |
| Imports Me | |
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| 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 |
| 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 |