TimeSeriesExperiment

DOI: 10.18129/B9.bioc.TimeSeriesExperiment    

This package is for version 3.15 of Bioconductor; for the 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")

 

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

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) (4 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
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_1.13.0.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
Package Short Url https://bioconductor.org/packages/TimeSeriesExperiment/
Package Downloads Report Download Stats

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