TimeSeriesExperiment

DOI: 10.18129/B9.bioc.TimeSeriesExperiment    

Analysis for short time-series data

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("TimeSeriesExperiment")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TimeSeriesExperiment", version = "3.8")

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 1.0.1
License LGPL (>= 3)
Depends R (>= 3.5.1), 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_1.0.1.tar.gz
Windows Binary TimeSeriesExperiment_1.0.1.zip
Mac OS X 10.11 (El Capitan) TimeSeriesExperiment_1.0.1.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 http://bioconductor.org/packages/TimeSeriesExperiment/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: