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 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.