TimeSeriesExperiment

DOI: 10.18129/B9.bioc.TimeSeriesExperiment    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TimeSeriesExperiment.

Analysis for short time-series data

Bioconductor version: 3.11

Visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.

Author: Lan Huong Nguyen

Maintainer: Lan Huong Nguyen <nlhuong90 at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Gene expression time course data analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Microbiome, Normalization, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.8 (R-3.5) (2 years)
License	LGPL (>= 3)
Depends	R (>= 3.5.0), 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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TimeSeriesExperiment_1.6.0.tar.gz
Windows Binary	TimeSeriesExperiment_1.6.0.zip
macOS 10.13 (High Sierra)	TimeSeriesExperiment_1.6.0.tgz
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