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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CountClust")
AuthorKushal Dey [aut, cre], Joyce Hsiao [aut], Matthew Stephens [aut]
Bioconductor views Clustering GeneExpression RNASeq Sequencing Software StatisticalMethod Visualization
Date of publicationNone
MaintainerKushal Dey <kkdey@uchicago.edu>
LicenseGPL (>= 2)
Version1.3.0
https://github.com/kkdey/CountClust

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BatchCorrectedCounts.R R/ExtractHighCorFeatures.R R/ExtractTopFeatures.R R/FitGoM.R R/RemoveSparseFeatures.R R/StructureGGplot.R R/Structure_omega.R R/cg_topics.R R/compGoM.R R/compare_omega.R R/data.R R/handleNA.R R/nullmodel_GoM.R
README.md
build
build/vignette.rds
data
data/AbundanceGoM.rda
data/GTExV6Brain.FitGoM.rda
data/MouseDeng2014.FitGoM.rda
data/MouseJaitinSpleen.FitGoM.rda
data/datalist
data/ex.counts.rda
inst
inst/doc
inst/doc/count-clust.R
inst/doc/count-clust.Rnw
inst/doc/count-clust.pdf
man
man/AbundanceGoM.Rd man/BatchCorrectedCounts.Rd man/ExtractTopFeatures.Rd man/FitGoM.Rd man/GTExV6Brain.FitGoM.Rd man/MouseDeng2014.FitGoM.Rd man/MouseJaitinSpleen.FitGoM.Rd man/RemoveSparseFeatures.Rd man/StructureGGplot.Rd man/Structure_omega.Rd man/cg_topics.Rd man/compare_omega.Rd man/ex.counts.Rd man/handleNA.Rd man/nullmodel_GoM.Rd
update_remotes.sh
vignettes
vignettes/count-clust-concordance.tex
vignettes/count-clust.Rnw
vignettes/figures
vignettes/figures/gtex_annot-1.png
vignettes/figures/plot_topic-1.png
vignettes/figures/plot_topic_2-1.png
vignettes/figures/plot_topic_deng-1.png
vignettes/figures/plot_topic_gtex-1.png
vignettes/structure_plot.png
vignettes/test
vignettes/test/countsclust.R vignettes/test/data_prepare.R
vignettes/test/metadata_brain.txt
vignettes/test/polarHistogramStructure.R
vignettes/test/samples_id.txt
vignettes/test/structure_plot.pdf
vignettes/test/structure_plot.png
vignettes/test/test_code.R vignettes/test/test_code_2.R vignettes/test/test_code_3.R vignettes/test/test_code_4.R

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