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

DOI: 10.18129/B9.bioc.TimeSeriesExperiment

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

Need some help? Ask on the Bioconductor Support site!

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

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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