CountClust
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CountClust.
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Bioconductor version: 3.9
Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression count data, identifies characteristic genes driving cluster memberships, and provides a visual summary of the cluster memberships.
Author: Kushal Dey [aut, cre], Joyce Hsiao [aut], Matthew Stephens [aut]
Maintainer: Kushal Dey <kkdey at uchicago.edu>
citation("CountClust")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CountClust")
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("CountClust")| Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.4), ggplot2 (>= 2.1.0) |
| Imports | SQUAREM, slam, maptpx, plyr (>= 1.7.1), cowplot, gtools, flexmix, picante, limma, parallel, reshape2, stats, utils, graphics, grDevices |
| System Requirements | |
| URL | https://github.com/kkdey/CountClust |
See More
| Suggests | knitr, kableExtra, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable |
| 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 | CountClust_1.12.0.tar.gz |
| Windows Binary | CountClust_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | CountClust_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CountClust |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CountClust |
| Bioc Package Browser | https://code.bioconductor.org/browse/CountClust/ |
| Package Short Url | https://bioconductor.org/packages/CountClust/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |