| ccfindR-package | ccfindR: Cancer Clone FindeR |
| assignCelltype | Cell type assignment via GSEA |
| 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 |
| 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-method | Coefficient matrix accessor |
| coeff<- | Generics for coefficient matrix assignment |
| coeff<--method | Modify coefficient matrices |
| colData-method | Sample annotation accessor |
| colData<--method | Cell annotation assignment |
| counts-method | Accessor for count matrix |
| counts<--method | Assignment of count matrix |
| dbasis | Basis SD matrix accessor |
| dbasis-method | Basis SD matrix accessor |
| dbasis<- | Basis SD matrix assignment |
| dbasis<--method | Modify dbasis matrices |
| dcoeff | Coeff SD matrix accessor |
| dcoeff-method | Coeffcient SD matrix accessor |
| dcoeff<- | Coeff SD matrix assignment |
| dcoeff<--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-method | Rank measure accessor |
| measure<- | Generics for factorization measure assignment |
| measure<--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-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 | Feature 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 |
| write_meta | Write meta genes to a file |
| [-method | Subsetting scNMFSet object |