TimeSeriesExperiment

This package is for version 3.15 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: 3.15

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 (from within R, enter 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TimeSeriesExperiment")
Gene expression time course data analysis HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Microbiome, Normalization, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization
Version 1.13.0
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
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TimeSeriesExperiment_1.13.0.tar.gz
Windows Binary
macOS Binary (x86_64) TimeSeriesExperiment_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TimeSeriesExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TimeSeriesExperiment
Bioc Package Browser https://code.bioconductor.org/browse/TimeSeriesExperiment/
Package Short Url https://bioconductor.org/packages/TimeSeriesExperiment/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive