CountClust

This package is for version 3.7 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: 3.7

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 (from within R, enter citation("CountClust")):

Installation

To install this package, start R (version "3.5") 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 PDF
NEWS Text

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, StatisticalMethod, Visualization
Version 1.8.0
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
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Suggests knitr, kableExtra, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable
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Package Archives

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

Source Package CountClust_1.8.0.tar.gz
Windows Binary CountClust_1.8.0.zip
Mac OS X 10.11 (El Capitan) CountClust_1.8.0.tgz
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
Old Source Packages for BioC 3.7 Source Archive