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

DOI: 10.18129/B9.bioc.CountClust

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 (from within R, enter 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

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

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_1.12.0.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/

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Old Source Packages for BioC 3.9 Source Archive