Man pages for mariiabilous/SuperCellBM
| add_cor_pval | computes p value of gene gene correlations |
| all_gene_cor | Computes gene-gene correlations |
| all_gene_cor_with_pval | Computes gene-gene correlations and p values |
| annotate_supercells_to_cluster | Computes annotation of super-cell types based on the... |
| bind_by_graining_level | Concatenates super-cell-like structures by graining level |
| bind_by_method | Concatenates super-cell-like structures by method |
| bind_by_seed | Concatenates super-cell-like structures by seeds |
| build_MC | Build metacell oblect Wrapper that inits and builds metacell... |
| compute_alternative_clustering | Compute alternative clustering at single-cell level |
| compute_alternative_SC | Compute super-cells using alternative algorithms behind.... |
| compute_consistency_of_supercell_clustering | Compute consistency of super-cell (meta-cell) clustering with... |
| compute_consistency_of_supercell_DEA | Compute consistency of super-cell (meta-cell) DEA with the GT... |
| compute_consistency_of_supercell_optimal_clustering | Compute consistency of super-cell (meta-cell) clustering... |
| compute_DEA_GT_bool | Compute bool vector of cluster-specific DEG |
| compute_singglecell_DEA | Computes DEA for single-cell data and for GT cell type... |
| compute_singlecell_silh | Computes silhouette width for a sequence of single-cell... |
| compute_singlecell_unweighted_clustering | Coumputes unweighted clustering for single-cell data |
| compute_supercells | Computes super-cells for the Exact, Approximate super-cells... |
| compute_supercells_additional_gammas | Computed super-cells for the additional gamma as concatenates... |
| compute_supercells_additional_seeds | Computed super-cells for the additional seeds and... |
| compute_supercells_clustering | Computes clustering for super-cells |
| compute_supercells_DEA | Computes differential expression analysis for super-cells |
| compute_supercells_GE | Computes gene expression of metacells |
| compute_supercells_metacells | compute super-cell like structure of metacells |
| compute_supercells_metacells_with_min_mc_size | compute super-cell like structure of metacells (based on... |
| compute_supercells_PCA | Computes PCA for supee-cells over all simplification methods,... |
| compute_supercells_silhouette | Computes silhouete distance for a list of clustring results |
| compute_supercells_unweighted_clustering | Coumputes unweighted clustering for super-cell-like list |
| diag_consistency_mtrx | Diagonalize two clustering consistency matricies to map... |
| get_actual_gammas_metacell | returns list of actual gammas of metacells |
| get_GO | Retreives and saves GO data |
| get_SC_by_gamma | Returns super-cell-like structure at specific graining levels |
| GO_match_summary | Computes mean and median values of jaccard GO match score... |
| GO_match_top_cor_genes | computes jaccard index of GO annotation of a pair of genes,... |
| Graph_to_igraph | Convert \list[SeuratObject]Graph to \list[igraph]igraph |
| hello | Hello, World! |
| init_mc | Initiate MC folders |
| map_clustering_to_cell_type | Map super-cell clustering results to GT cell type annotation |
| mc_build_cgraph | Builds cell graph object using Metacell package |
| mc_build_mc | Builds metacell partition using output of 'mc_build_cgraph' |
| plot_annotation_purity | Plots super-cell purity |
| plot_argmax_silh | Plots optimal number of clusters (as argmax of silhouette... |
| plot_argmax_silh_alt_clusterings | Plots optimal number of clusters (as argmax of silhouette... |
| plot_clustering_consistency | Plot clustering consistency |
| plot_DEA_consistency | Plot DEA consistency |
| plot_GO_match_score | Plot (normalized) GO match score |
| plot_legend_celltype | Plots and saves a legend mapping cell types and colors |
| plot_supercell_size_distribution | Plot super-cell size distribution |
| rank_gene_gene_cor | rank gene-gene correlation |
| remove_mc_fields | Remove MC field from SC.list object when not needed anymore... |
| SCBM_saveplot | Saves plot for manuscript |
| SC_from_membership | Builds super-cell object from a single-cell NW and a... |
| SCimple2Metacell | Computes metacell from super-cells |
| SCimple2Random | from Scimplify result to random simplification |
| SCimple2Subsampling | rom Scimplify result to subsampling |
