CountClust

DOI: 10.18129/B9.bioc.CountClust    

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

Bioconductor version: Release (3.8)

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:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CountClust", version = "3.8")

Documentation

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

browseVignettes("CountClust")

 

HTML R Script Vignette Title
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, StatisticalMethod, Visualization
Version 1.10.0
In Bioconductor since BioC 3.3 (R-3.3) (2.5 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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CountClust_1.10.0.tar.gz
Windows Binary CountClust_1.10.0.zip
Mac OS X 10.11 (El Capitan) CountClust_1.10.0.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 http://bioconductor.org/packages/CountClust/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: