TimeSeriesExperiment
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TimeSeriesExperiment.
Analysis for short time-series data
Bioconductor version: 3.16
TimeSeriesExperiment is a visualization and analysis toolbox for short time course data. The package includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. Additionally, it also provides methods for retrieving enriched pathways.
Author: Lan Huong Nguyen [cre, aut] 
Maintainer: Lan Huong Nguyen <nlhuong90 at gmail.com>
citation("TimeSeriesExperiment")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TimeSeriesExperiment")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Microbiome, Normalization, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1), S4Vectors(>= 0.19.23), SummarizedExperiment(>= 1.11.6) |
| Imports | dynamicTreeCut, dplyr, edgeR, DESeq2, ggplot2 (>= 3.0.0), graphics, Hmisc, limma, methods, magrittr, proxy, stats, tibble, tidyr, vegan, viridis, utils |
| System Requirements | |
| URL | https://github.com/nlhuong/TimeSeriesExperiment |
| Bug Reports | https://github.com/nlhuong/TimeSeriesExperiment/issues |
See More
| Suggests | Biobase, BiocFileCache(>= 1.5.8), circlize, ComplexHeatmap, GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db, MASS, RColorBrewer, rmarkdown, UpSetR |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/TimeSeriesExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TimeSeriesExperiment |
| Package Short Url | https://bioconductor.org/packages/TimeSeriesExperiment/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |