basis | Basis matrices in an Object |
basis-method | Basis matrix accessor |
basis<- | Generics for basis matrix assignment |
basis<--method | Modify basis matrices |
build_tree | Build tree connecting clusters at different ranks |
cell_map | Plot heatmap of clustering coefficient matrix |
cluster_id | Assign cells into clusters |
coeff | Coefficient matrices in an Object |
coeff-method | Coefficient matrix accessor |
coeff<- | Generics for coefficient matrix assignment |
coeff<--method | Modify coefficient matrices |
colData-method | Cell annotation accessor |
colData<--method | Cell annotation assignment |
counts-method | Accessor for count matrix |
counts<--method | Assignment of count matrix |
factorize | Maximum likelihood factorization |
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-method | Rank measure accessor |
measure<- | Generics for factorization measure assignment |
measure<--method | Modify factorization measure |
meta_genes | Find metagenes from basis matrix |
normalize_count | Normalize count data |
plot-method | Class 'scNMFSet' for storing input data and results |
plot_genes | Plot gene variance distributions |
plot_tree | Plot cluster tree |
ranks | Rank values in an Object |
ranks-method | Rank accessor |
ranks<- | Generics for ranks assignment |
ranks<--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-method | Gene annotation accessor |
rowData<--method | Gene annotation assignment |
scNMFSet | Create 'scNMFSet' object |
scNMFSet-class | Class 'scNMFSet' for storing input data and results |
show-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 |
[-method | Subsetting scNMFSet object |