splineTimeR

DOI: 10.18129/B9.bioc.splineTimeR    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see splineTimeR.

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Bioconductor version: 3.10

This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.

Author: Agata Michna

Maintainer: Herbert Braselmann <braselm at helmholtz-muenchen.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("splineTimeR")

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("splineTimeR")

 

PDF	R Script	splineTimeR
PDF		Reference Manual

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Regression, Software, TimeCourse
Version	1.14.0
In Bioconductor since	BioC 3.3 (R-3.3) (4 years)
License	GPL-3
Depends	R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
Imports
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
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Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	splineTimeR_1.14.0.tar.gz
Windows Binary	splineTimeR_1.14.0.zip
Mac OS X 10.11 (El Capitan)	splineTimeR_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/splineTimeR
Source Repository (Developer Access)	git clone [email protected]:packages/splineTimeR
Package Short Url	https://bioconductor.org/packages/splineTimeR/
Package Downloads Report	Download Stats