CountClust

DOI: 10.18129/B9.bioc.CountClust    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 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: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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

PDF		Reference Manual

Details

biocViews	Clustering, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod, Visualization
Version	1.23.1
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 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
LinkingTo
Suggests	knitr, kableExtra, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable
SystemRequirements
Enhances
URL	https://github.com/kkdey/CountClust
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Package Archives

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

Source Package
Windows Binary	CountClust_1.23.1.zip
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/CountClust
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CountClust
Package Short Url	https://bioconductor.org/packages/CountClust/
Package Downloads Report	Download Stats