splineTimeR

This is the released version of splineTimeR; for the devel version, see splineTimeR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

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

Bioconductor version: Release (3.23)

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 <hbraselmann at online.de>, Martin Selmansberger <martin.selmansberger at helmholtz-muenchen.de>

Citation (from within R, enter citation("splineTimeR")):

Agata Michna. splineTimeR: Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction. doi:10.18129/B9.bioc.splineTimeR, R package version 1.40.0, https://bioconductor.org/packages/splineTimeR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

splineTimeR	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Regression, Software, TimeCourse
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL-3
Depends	R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
Imports
System Requirements
URL

Suggests	knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	splineTimeR_1.40.0.tar.gz
Windows Binary (x86_64)	splineTimeR_1.40.0.zip
macOS Binary (big-sur-x86_64)	splineTimeR_1.40.0.tgz
macOS Binary (sonoma-arm64)	splineTimeR_1.40.0.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