[,scNMFSet,ANY,ANY,ANY-method
                        Subsetting scNMFSet object
assignCelltype          Cell type assignment via GSEA
basis                   Basis matrices in an Object
basis,scNMFSet-method   Basis matrix accessor
basis<-                 Generics for basis matrix assignment
basis<-,scNMFSet-method
                        Modify basis matrices
build_tree              Build tree connecting clusters at different
                        ranks
ccfindR                 ccfindR: Cancer Clone FindeR
cell_map                Plot heatmap of clustering coefficient matrix
cluster_id              Assign cells into clusters
coeff                   Coefficient matrices in an Object
coeff,scNMFSet-method   Coefficient matrix accessor
coeff<-                 Generics for coefficient matrix assignment
coeff<-,scNMFSet-method
                        Modify coefficient matrices
colData,scNMFSet-method
                        Sample annotation accessor
colData<-,scNMFSet,ANY-method
                        Cell annotation assignment
counts,scNMFSet-method
                        Accessor for count matrix
counts<-,scNMFSet-method
                        Assignment of count matrix
dbasis                  Basis SD matrix accessor
dbasis,scNMFSet-method
                        Basis SD matrix accessor
dbasis<-                Basis SD matrix assignment
dbasis<-,scNMFSet-method
                        Modify dbasis matrices
dcoeff                  Coeff SD matrix accessor
dcoeff,scNMFSet-method
                        Coeffcient SD matrix accessor
dcoeff<-                Coeff SD matrix assignment
dcoeff<-,scNMFSet-method
                        Modify dcoeff matrices
factorize               Maximum likelihood factorization
feature_map             Plot heatmap of basis matrix
filter_cells            Filter cells with quality control criteria
filter_genes            Filter genes with quality control criteria
gene_map                Plot heatmap of metagene matrix
measure                 Factorization measures in an Object
measure,scNMFSet-method
                        Rank measure accessor
measure<-               Generics for factorization measure assignment
measure<-,scNMFSet-method
                        Modify factorization measure
meta_gene.cv            Meta gene table with CV
meta_genes              Find metagenes from basis matrix
newick                  Generate Newick format tree string from tree
                        list object
normalize_count         Normalize count data
optimal_rank            Determine optimal rank
plot_genes              Plot gene variance distributions
plot_tree               Plot cluster tree
ranks                   Rank values in an Object
ranks,scNMFSet-method   Rank accessor
ranks<-                 Generics for ranks assignment
ranks<-,scNMFSet-method
                        Modify ranks
read_10x                Read 10x data and generate scNMF object
remove_zeros            Remove rows or columns that are empty from an
                        object
rename_tips             Rename tips of trees with cell types
rowData,scNMFSet-method
                        Feature annotation accessor
rowData<-,scNMFSet-method
                        Gene annotation assignment
scNMFSet                Create 'scNMFSet' object
scNMFSet-class          Class 'scNMFSet' for storing input data and
                        results
show,scNMFSet-method    Display object
simulate_data           Generate simulated data for factorization
simulate_whx            Simulate factor matrices and data using priors
vb_factorize            Bayesian NMF inference of count matrix
visualize_clusters      Visualize clusters
write_10x               Write 10x data files
write_meta              Write meta genes to a file
