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

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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]
Date of publication
None
Maintainer
Kushal Dey <kkdey@uchicago.edu>
License
GPL (>= 2)
Version
1.2.0
URLs

View on Bioconductor

Man pages

AbundanceGoM
GoM model fit for abundance data
BatchCorrectedCounts
Obtain Batch effect Corrected counts
cg_topics
Compute the center of gravity of the clusters
compare_omega
Re-ordering cluster membership proportion matrices and...
ex.counts
counts data for GTEx V6 Brain data for 200 genes
ExtractTopFeatures
Extracting top driving genes driving GoM clusters
FitGoM
Grade of Membership (GoM) model fit !
GTExV6Brain.FitGoM
GoM model fit for GTEx V6 Brain bulk-RNA data
handleNA
Deal with NAs in the dataset!
MouseDeng2014.FitGoM
GoM model fit for Deng et al 2014 single cell RNA-seq data on...
MouseJaitinSpleen.FitGoM
GoM model fit for Jaitin et al 2014 single cell RNA-seq data...
nullmodel_GoM
Null models for Grade of Membership (GoM) cluster validation
RemoveSparseFeatures
Removes features with a lot of 0 counts
StructureGGplot
Struture plot with ggplot2 package
Structure_omega
Structure Plot of GoM model proportions (Base plot version)!

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