Man pages for diem
Debris-Containing Droplet Identification using EM
| barcode_rank_plot | Create a barcode rank plot |
| call_targets | Call clean droplets after running EM |
| convert_to_seurat | Convert an SCE object to Seurat |
| create_SCE | Create an SCE object from a sparse matrix |
| diem | Run DIEM pipeline |
| divide_by_colsum | Divide elements of a column by the column's sum in a sparse... |
| dmmn | Compute density of multinomial mixture for a matrix |
| dmultinom_sparse | Get log multinomial density of columns in a sparse matrix. |
| droplet_data | Return the droplet data from an SCE object |
| em | EM function |
| e_step_mn | Computed expected log likelihood of multinomial mixture |
| 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_clean_ids | Return IDs of clean droplets |
| get_gene_pct | Get percent of reads align to given gene(s) |
| get_knn | Get k-nearest neighbor graph |
| get_removed_ids | Return IDs of removed droplets |
| get_var_genes | Get variable genes |
| initialize_clusters | Initialize clustering for EM |
| init_param | Initialize EM parameters given group assignments |
| mb_small | Single-nucleus RNA-seq of mouse brain |
| m_step_mn | Maximize multinomial parameters in EM |
| normalize_data | Normalize raw counts. |
| norm_counts | Normalize counts of a sparse matrix |
| plot_umi_gene | Scatterplot of genes vs. UMI counts, colored by posterior... |
| plot_umi_gene_call | Scatterplot of genes vs. UMI counts, colored by call |
| raw_counts | Return raw counts |
| read_10x | Read 10X counts data |
| run_em | Run EM on counts to estimate multinomial mixture model |
| SCE-class | SCE |
| set_cluster_set | Set droplets for cluster initialization |
| set_debris_test_set | Set debris and test droplets |
| sum_log | sum of logs |
