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| Alpha | Get Alpha parameters for clusters |
| alpha_max_loo | Maximize leave-one-out with respect to alpha |
| alpha_mom | Estimate alpha using method of moments |
| barcode_rank_plot | Create a barcode rank plot |
| call_targets | Call clean droplets after running EM |
| check_k_init | Check values of given k_init against kruns |
| condense_labs | Re-assign labels by condensing to 1 to k |
| convert_to_seurat | Convert an SCE object to Seurat |
| create_SCE | Create an SCE object from a sparse matrix |
| diem | Run DIEM pipeline |
| distances | Get cluster distances to background |
| divide_by_colsum | Divide elements of a column by the column's sum in a sparse matrix |
| droplet_data | Return the droplet data from an SCE object |
| em | Run EM |
| fill_counts | Fill information from raw counts |
| filter_genes | Filter out lowly expressed genes |
| fraction_log | fraction of logs |
| gene_data | Return the gene data from an SCE object |
| get_alpha | Get MLE of alphas |
| get_clean_ids | Return IDs of clean droplets |
| get_dist | Get cluster distances to background disrtibution |
| get_gene_pct | Get percent of reads aligned to given gene(s) |
| get_llk | Get log likelihood under Dirichlet-multinomial |
| get_pcs | Get PCs |
| get_pi | Get mixing coefficients of Mixture model from posterior probabilities Z |
| get_removed_ids | Return IDs of removed droplets |
| get_var_genes | Get variable genes |
| get_z | Get posterior probabilities from log likelihoods and mixing coefficients |
| init | Initialize clusters |
| mb_small | Single-nucleus RNA-seq of mouse brain |
| merge_size | Merge small clusters |
| normalize_data | Normalize raw counts. |
| norm_counts | Normalize counts of a sparse matrix |
| plot_dist | plot dist values against counts |
| plot_umi_gene | Scatterplot of genes vs. UMI counts, colored by posterior probability |
| plot_umi_gene_call | Scatterplot of genes vs. UMI counts, colored by call |
| raw_counts | Return raw counts |
| read_10x | Read 10X counts data |
| rm_close | Remove clusters close to the background distribution |
| run_em | Run EM |
| run_pca | Run PCA |
| SCE | SCE |
| SCE-class | SCE |
| set_debris_test_set | Set debris and test droplets |
| sum_log | sum of logs |
| z_table | Return design matrix of labs vector |