splineTimeR
This is the development version of splineTimeR; for the stable release version, see splineTimeR.
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Bioconductor version: Development (3.24)
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("splineTimeR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Regression, Software, TimeCourse |
| Version | 1.41.0 |
| 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 |
See More
| Suggests | knitr |
| 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 | splineTimeR_1.41.0.tar.gz |
| Windows Binary (x86_64) | splineTimeR_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | splineTimeR_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | splineTimeR_1.41.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/splineTimeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/splineTimeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/splineTimeR/ |
| Package Short Url | https://bioconductor.org/packages/splineTimeR/ |
| Package Downloads Report | Download Stats |