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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 |
| assign_clusters | Assign clusters to droplets from EM |
| barcode_rank_plot | Create a barcode rank plot |
| call_targets | Call clean droplets after running EM using percent debris |
| clusters | Get cluster labels |
| 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 |
| debris_genes | Return the differentially expression results for debris genes |
| de_basic | Run a basic DE between clusters |
| de_ttest | Run a DE between two groups with Welch's t-test |
| de_ttest_all | Run a DE across clusters with Welch's t-test |
| 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 |
| estimate_dbr_score | Estimate debris score per droplet |
| 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_dm | Get MLE of alphas |
| get_alpha_mult | Get MLE of multinomial alphas |
| get_clean_ids | Return IDs of clean droplets |
| get_gene_pct | Get percent of reads aligned to given gene(s) |
| get_llk | Get log likelihood |
| 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_clust | Scatterplot of cluster means for indicated variables |
| plot_data | Scatterplot of features from meta data or gene expression |
| plot_dbr_score | Scatterplot of debris score against feature |
| plot_umi_gene | Scatterplot of genes vs. UMI count |
| raw_counts | Return raw counts |
| read_10x | Read 10X counts data |
| run_em | Run EM |
| run_pca | Run PCA |
| SCE | SCE |
| SCE-class | SCE |
| set_debris_test_set | Set debris and test droplets |
| summarize_clusters | Output summary stats from a DIEM run |
| sum_log | sum of logs |
| top_genes | Get top up-regulated genes per cluster |
| z_table | Return design matrix of labs vector |