splineTimeR

DOI: 10.18129/B9.bioc.splineTimeR    

This package is for version 3.9 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: 3.9

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	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 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
Links To Me
Build Report

Package Archives

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

Source Package	splineTimeR_1.12.0.tar.gz
Windows Binary	splineTimeR_1.12.0.zip
Mac OS X 10.11 (El Capitan)	splineTimeR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/splineTimeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/splineTimeR
Package Short Url	https://bioconductor.org/packages/splineTimeR/
Package Downloads Report	Download Stats