CountClust

This package is for version 3.14 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: 3.14

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 "4.1") 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

Reference Manual PDF

Details

biocViews Clustering, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod, Visualization
Version 1.22.0
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
Windows Binary
macOS 10.13 (High Sierra)
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/
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Old Source Packages for BioC 3.14 Source Archive