CountClust

DOI: 10.18129/B9.bioc.CountClust    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CountClust.

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

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 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_1.12.0.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
Package Short Url	https://bioconductor.org/packages/CountClust/
Package Downloads Report	Download Stats