Cancer Clone Finder

assignCelltype | Cell type assignment via GSEA |

basis | Basis matrices in an Object |

basis-scNMFSet-method | Basis matrix accessor |

basis-set | Generics for basis matrix assignment |

basis-set-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-set | Generics for coefficient matrix assignment |

coeff-set-scNMFSet-method | Modify coefficient matrices |

colData-scNMFSet-method | Sample annotation accessor |

colData-set-scNMFSet-ANY-method | Cell annotation assignment |

counts-scNMFSet-method | Accessor for count matrix |

counts-set-scNMFSet-method | Assignment of count matrix |

dbasis | Basis SD matrix accessor |

dbasis-scNMFSet-method | Basis SD matrix accessor |

dbasis-set | Basis SD matrix assignment |

dbasis-set-scNMFSet-method | Modify dbasis matrices |

dcoeff | Coeff SD matrix accessor |

dcoeff-scNMFSet-method | Coeffcient SD matrix accessor |

dcoeff-set | Coeff SD matrix assignment |

dcoeff-set-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-set | Generics for factorization measure assignment |

measure-set-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-set | Generics for ranks assignment |

ranks-set-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-set-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 |

subset-methods | Subsetting scNMFSet object |

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 |

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