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


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Documentation for package ‘CountClust’ version 1.2.0

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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 Information calculation
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 mouse
MouseJaitinSpleen.FitGoM GoM model fit for Jaitin et al 2014 single cell RNA-seq data on mouse
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