TMixClust
This is the released version of TMixClust; for the devel version, see TMixClust.
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Bioconductor version: Release (3.23)
Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.
Author: Monica Golumbeanu <golumbeanu.monica at gmail.com>
Maintainer: Monica Golumbeanu <golumbeanu.monica at gmail.com>
citation("TMixClust")):
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")
BiocManager::install("TMixClust")
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("TMixClust")| Clustering time series gene expression data with TMixClust | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneExpression, Software, StatisticalMethod, TimeCourse |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.4) |
| Imports | gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, knitr, BiocStyle, testthat |
| 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 | TMixClust_1.34.0.tar.gz |
| Windows Binary (x86_64) | TMixClust_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | TMixClust_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | TMixClust_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TMixClust |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TMixClust |
| Bioc Package Browser | https://code.bioconductor.org/browse/TMixClust/ |
| Package Short Url | https://bioconductor.org/packages/TMixClust/ |
| Package Downloads Report | Download Stats |