TimeSeriesExperiment

This package is for version 3.9 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: 3.9

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 "3.6") 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

Details

biocViews Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Microbiome, Normalization, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
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_1.2.0.tar.gz
Windows Binary TimeSeriesExperiment_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) TimeSeriesExperiment_1.2.0.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 3.9 Source Archive