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.

AuthorKushal Dey [aut, cre], Joyce Hsiao [aut], Matthew Stephens [aut]
Date of publicationNone
MaintainerKushal Dey <kkdey@uchicago.edu>
LicenseGPL (>= 2)
Version1.2.0
https://github.com/kkdey/CountClust

View on Bioconductor

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.