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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CountClust")
In most cases, you don't need to download the package archive at all.
CountClust
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This package is for version 3.4 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: 3.4
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("https://bioconductor.org/biocLite.R")
biocLite("CountClust")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CountClust")
| R Script | Grade of Membership Clustering and Visualization using CountClust | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, GeneExpression, RNASeq, Sequencing, Software, StatisticalMethod, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1 year) |
| 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.
| Package Source | CountClust_1.2.0.tar.gz |
| Windows Binary | CountClust_1.2.0.zip |
| Mac OS X 10.9 (Mavericks) | CountClust_1.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CountClust/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/CountClust/ |
| Package Downloads Report | Download Stats |
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