splineTimeR

DOI: 10.18129/B9.bioc.splineTimeR    

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

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("splineTimeR")

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	1.6.0
In Bioconductor since	BioC 3.3 (R-3.3) (2 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
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	splineTimeR_1.6.0.tar.gz
Windows Binary	splineTimeR_1.6.0.zip
Mac OS X 10.11 (El Capitan)	splineTimeR_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/splineTimeR
Package Short Url	http://bioconductor.org/packages/splineTimeR/
Package Downloads Report	Download Stats