TimeSeriesExperiment

DOI: 10.18129/B9.bioc.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: Release (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>

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

PDF		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) (4.5 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
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/nlhuong/TimeSeriesExperiment
BugReports	https://github.com/nlhuong/TimeSeriesExperiment/issues
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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