To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CountClust")

In most cases, you don't need to download the package archive at all.

CountClust

DOI: 10.18129/B9.bioc.CountClust    

This is the development version of CountClust; for the stable release version, see CountClust.

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

Bioconductor version: Development (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CountClust")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CountClust")

 

PDF R Script Grade of Membership Clustering and Visualization using CountClust
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, StatisticalMethod, Visualization
Version 1.3.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.3.0), ggplot2 (>= 2.1.0)
Imports maptpx, slam, plyr (>= 1.7.1), cowplot, gtools, flexmix, picante, limma, parallel, reshape2, stats, utils, graphics, grDevices
LinkingTo
Suggests knitr, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable
SystemRequirements
Enhances
URL https://github.com/kkdey/CountClust
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package CountClust_1.3.0.tar.gz
Windows Binary CountClust_1.3.0.zip
Mac OS X 10.11 (El Capitan) CountClust_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CountClust
Package Short Url http://bioconductor.org/packages/CountClust/
Package Downloads Report Download Stats

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