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("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 | ||
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |