| allrow_cor | computing correlations between all rows in two matrices |
| gen_10x_mars_gene_match | Generate mapping of 10x to mars names |
| gset_add_genes | Add specific genes to the set |
| gset_get_feat_mat | extract umi matrix for the genes in the set, possibly... |
| gset_get_genes | Get genes of one set |
| gset_import_table | Import gene set for a text table |
| gset_new_gset | Generating a new gset |
| gset_new_restrict_gset | Generate a new gene set from an existing one, filtered by a... |
| gset_new_restrict_nms | Generate a new gene set from an existing one, filtered by a... |
| gset_write_table | Exprt gene set to a table |
| initialize-tgCellGraph-method | This constructs graph object from a data frame on columns... |
| initialize-tgCoClust-method | Construct a coclust object |
| initialize-tgGeneSets-method | tgGeneSets public constructor |
| initialize-tgMC2D-method | Construct a meta cell 2D embedding |
| initialize-tgMCAtlas-method | Construct a meta cell reference atlas |
| initialize-tgMCCov-method | Construct a meta cell object |
| initialize-tgMCManifGraph-method | Construct a meta cell manifold graph |
| initialize-tgMCTNetwork-method | Construct a meta cell time network |
| mcatlas_annotate_mc_by_mc2mc_projection | Annotate query metacell with atlas by comparing query... |
| mcatlas_annotate_mc_by_sc2mc_projection | Annotate query metacell with atlas by comparing query cells... |
| mcatlas_annotate_mc_by_sc2sc_projection | Annotate query metacell with atlas by comparing query cells... |
| mcatlas_comp_adj_type_n | Compute the summary matrix of cell type adjacencies |
| mcatlas_project_query | Compute association of query umi matrix and atlas |
| mc_colorize | colorize metacell using a set of prefered markers and their... |
| mc_colorize_default | colorize metacell using an ugly default color spectrum, or a... |
| mc_colorize_from_ref_mc | colorize metacell by projecting colors from another metacell... |
| mc_colorize_sup_hierarchy | colorize metacells using a set of super MCs derived by... |
| mc_compute_cov_gc | Compute fraction of non zero expressing cells per gene and mc |
| mc_compute_e_gc | Compute metacell absolute mean umi per cell |
| mc_compute_fp | Compute metacell gene footprint |
| mc_compute_n_bc | Compute distribution of cells over batches and metacell |
| mc_compute_outlier_fc | Compute log fold change expression of each gene given its... |
| mcell_add_cgraph_bknn_norm_mc | Build a cell graph using balanced knn after normalizing over... |
| mcell_add_cgraph_from_distmat | Build a cell graph using blanacing of an extrenal distance... |
| mcell_add_cgraph_from_mat_bknn | Build a cell graph using balanced knn graph on given gene... |
| mcell_add_cgraph_from_mat_raw_knn | Build a cell graph using raw knn graph on given gene features |
| mcell_add_gene_names_xref_mars10x | Create a gene name xref for heuristc map of mars/10x |
| mcell_add_gene_stat | mcell_gene_stat |
| mcell_add_mars_facs_data | Creates a new matrix object from a given one by adding FACS... |
| mcell_add_mc_from_graph | Compute metacell using a native implementation of a graph... |
| mcell_batch_stats | generate a batch stat table for a given single cell umi... |
| mcell_calc_one_batch_stats | calc batch stats - essentially umi distribution |
| mcell_cgraph_norm_gcor | Computing gene-gene correlation normaized over a similarity... |
| mcell_coclust_filt_by_k_deg | Return a filter (boolean vector) selecting only coclust edges... |
| mcell_coclust_from_graph_resamp | Compute metacell using resampling iterations of graph cover... |
| mcell_compare_bulk | Utility plot function to compare bulk expression of two... |
| mcell_gen_atlas | wrap up an atlas object from mc, mc2d and matrix ids |
| mcell_gen_cell_cor_gset | Compute a cell cell correlation matrix using features defined... |
| mcell_graph_pred_corr | Compute predictive value of MC cover as correlation of MC... |
| mcell_gset_add_gene | adding genes to a gene set |
| mcell_gset_filter_cov | gnereate/filter gene features from coverage threshold in... |
| mcell_gset_filter_multi | Select/filter gene features from using multiple statistics... |
| mcell_gset_filter_szcor | gnereate/filter gene features from statistics on correlation... |
| mcell_gset_filter_varmean | gnereate/filter gene features from gstat normalized var/mean |
| mcell_gset_from_mc_markers | Generate a gene set of markers from a metacell cover |
| mcell_gset_remove_clusts | add new gene set based on an existing one with filtering... |
| mcell_gset_split_by_dsmat | split gene set into several modules using clustering of genes... |
| mcell_import_multi_mars | Load a matrix from a MARS-seq multi-batch dataset. The scdb... |
| mcell_import_multi_scmat_10x | Load a matrix from a 10x multi-batch dataset. The scdb... |
| mcell_import_scmat_10x | Load a matrix from a 10x dataset. The scdb version of... |
| mcell_import_scmat_tsv | Load a matrix from a simple dense table with genes in rows... |
| mcell_mat_ignore_cells | Generate a new matrix object with a given ignore cell list |
| mcell_mat_ignore_genes | Generate a new matrix object with a given ignore gene list |
| mcell_mat_ignore_small_cells | Generate a new matrix object after removing cells without... |
| mcell_mat_rpt_cor_anchors | Find and report naive gene gene correlation over umi matrix |
| mcell_mc2d_force_knn | Metacell layout using force directed projection of a low... |
| mcell_mc2d_force_knn_on_cells | Compute cells 2d coordinates based on the mc graph when the... |
| mcell_mc2d_plot | Plot mc+cell graph using pre-defined mc colorization |
| mcell_mc2d_plot_by_factor | Plot mc+cells using pre-defined mc colorization, breakdown by... |
| mcell_mc2d_plot_gene | Plot the (log2) metacell footprint value of the selected gene... |
| mcell_mc2d_rotate | Rotatae/invert projection |
| mcell_mc_add_annot | Update metacell annotation |
| mcell_mc_add_color | Update metacells colors |
| mcell_mc_cell_homogeneity | Compute cell homogeneity - the fraction of intra mc edges per... |
| mcell_mc_coclust_confusion_mat | Compute confusion matrix on metacells using a coclustering... |
| mcell_mc_confusion_mat | Compute confusion matrix on metacells |
| mcell_mc_edge_density | for each MC we compute mean and variance of the intra-MC edge... |
| mcell_mc_export_tab | Output genes cell modules footprint matrix with metadata on... |
| mcell_mc_from_coclust_balanced | build a metacell cover from co-clust data through filtering... |
| mcell_mc_from_coclust_hc | build a metacell cover from a co-clust object using a simple... |
| mcell_mc_from_coclust_louv_sub | build a metacell cover from a big co-clust using louvain... |
| mcell_mc_hclust_confu | comput mc hierarchucal clustering using the normalized... |
| mcell_mc_hierarchy | identify super structure in an mc cover, based on hcluster of... |
| mcell_mc_match_graph | TEst if a graph object cover all cells in the mc |
| mcell_mc_plot_by_factor | plot a heatmap of number of cells per metacell and metadata... |
| mcell_mc_plot_confusion | plot a metacel confusion matrix |
| mcell_mc_plot_gg | Utility plot function to compare two genes based on mc_fp |
| mcell_mc_plot_hierarchy | plot super strucutre: super clust mc footprint, and selected... |
| mcell_mc_plot_marks | plot a marker heat map give a metacell object |
| mcell_mc_plot_submc_marks | plot a marker heat map for a subset of metacells - selecting... |
| mcell_mc_plot_vgels | plot a "gel" like diagram showing expression of a gene of... |
| mcell_mc_pred_corr | Compute predictive value of MC cover as correlation of MC... |
| mcell_mc_reorder_hc | Reorder metacells using hierarchical clustering |
| mcell_mc_screen_outliers_1gene_fold | Simple screen for outlier cells in a metacell cover, finding... |
| mcell_mc_split_by_color_group | Splits input metacell object into sub-objects by color group,... |
| mcell_mc_split_filt | Split and filter metacells using dbscan and outlier gene... |
| mcell_merge_mats | ncell_merge_mats: Merge two matrix using their ids in scdb.... |
| mcell_mgraph_knn | Compute metacell manifod graph using the confusion matrix of... |
| mcell_mgraph_logistic | Compute metacell manifold graph using logistic distances and... |
| mcell_new_mc | Generate a new metacell in scdb |
| mcell_new_mc2d | Generate a new metacell in scdb |
| mcell_new_mcatlas | Generate a new atlas in scdb |
| mcell_new_mc_mgraph | Generate a new metacell manifold graph object |
| mcell_new_mctnetwork | Generate a new network in scdb |
| mcell_pipe_mat2mc2d | Linear simple pipeline for turning a matrix to a MC and... |
| mcell_plot_batch_stats | plot batches stats |
| mcell_plot_cross_mc | Plotting a matrix of co-occurences between two metacell... |
| mcell_plot_gset_cor_mats | Plot gene set correlation matrices given a an scamt. See... |
| mcell_plot_gstats | plot gene/feature statistics |
| mcell_plot_outlier_heatmap | Plot and outlier heat map. |
| mcell_plot_umis_per_cell | Plot histogram of total number of umis per cell in the umis... |
| mcell_proj_on_atlas | Project a metacell object on a reference "atlas" |
| mcell_read_multi_scmat_10x | read multiple 10x umi matrices and merge them, based on a... |
| mcell_read_multi_scmat_mars | read multiple MARS umi matrices and merge them, based on a... |
| mcell_scmat_plot_cmp_kcor | Analyze cell cell cor |
| mcell_wgtmc_pred_corr | Compute predictive value of MC cover as correlation of... |
| mc_reorder | Reorder metacell data given defined order |
| mc_restrict | Create a metacell object on a subset of the MCs, with all... |
| mc_set_outlier_mc | Move all cels from specific metacells to the outliers |
| mctnetwork_clust_flows | Clustring MCs based on the flow graph |
| mctnetwork_comp_manifold_costs | Compute and update manifold costs for a mc time network |
| mctnetwork_comp_propagation | Compute matrices for forward and backwrd propagation using... |
| mctnetwork_gen_e_gmt_p | This generate two large matrices showing expression of genes... |
| mctnetwork_gen_gmod_mc_t | Given a list of genes and a matrix, this compute mean umi per... |
| mctnetwork_gen_mincost_flows | Compute mincost flow and update the mct objects with flows... |
| mctnetwork_gen_network | Compute and update network strcuture from mc, manifodld costs |
| mctnetwork_get_flow_mat | Compute matrix of flows between MCs in a given time point |
| mctnetwork_get_type_flows | Compute matrix of flows over cell types |
| mctnetwork_propogate_from_t | Compute backward and forward flow propgation of metacell... |
| mc_update_stats | Compute stats over metacell and update the object |
| metacell | metacell |
| pipe | Pipe operator |
| plot_color_bar | Plot a color bar with values |
| port_cor | port_cor matrix correlation wrap. Parameter selects which... |
| rescale_sparse_mat_cols | Efficient version for scaling all columns in a sparse matrix |
| scdb_add_cgraph | scdb_add_cgraph - add cgraph to the DB and cahce |
| scdb_add_coclust | scdb_add_coclust - add coclust to the DB and cahce |
| scdb_add_gene_names_xref | scdb_add_gene_names_xref - add a gene name xref tab to the DB... |
| scdb_add_gset | scdb_add_gset - add gset to the DB and cahce |
| scdb_add_gstat | scdb_add_gstat - add gstat to the DB and cahce |
| scdb_add_mat | scdb_add_mat - add amatrix to the DB - will save it and cache |
| scdb_add_mc | scdb_add_mc - add mc to the DB and cahce |
| scdb_add_mc2d | scdb_add_mc2d - add mc2d to the DB and cahce |
| scdb_add_mcatlas | scdb_add_mcatlas - add mcatlas to the DB and cahce |
| scdb_add_mctnetwork | scdb_add_mctnetwork - add mctnetwork to the DB and cahce |
| scdb_add_mgraph | scdb_add_mgraph - add mgraph to the DB and cahce |
| scdb_cgraph | scdb_cgraph - get a cgraph object |
| scdb_coclust | scdb_coclust - get a coclust object |
| scdb_del_cgraph | scdb_del_cgraph - del cgraph from the DB and cahce |
| scdb_del_coclust | scdb_del_coclust - del coclust from the DB and cahce |
| scdb_del_gene_names_xref | scdb_del_gene_names_xref - remove a gene names xref from the... |
| scdb_del_gset | scdb_del_gset - del gset from the DB and cahce |
| scdb_del_gstat | scdb_del_gstat - del gstat from the DB and cahce |
| scdb_del_mat | scdb_del_mat - remove a matrix from the DB (not just the... |
| scdb_del_mc | scdb_del_mc - del mc from the DB and cahce |
| scdb_del_mc2d | scdb_del_mc2d - del mc2d from the DB and cahce |
| scdb_del_mcatlas | scdb_del_mcatlas - del mcatlas from the DB and cahce |
| scdb_del_mctnetwork | scdb_del_mctnetwork - del mctnetwork from the DB and cahce |
| scdb_del_mgraph | scdb_del_mgraph - del mgraph from the DB and cahce |
| scdb_gene_names_xref | scdb_gene_names_xref - get gene names convertor table from db |
| scdb_gset | scdb_gset - get a gene set |
| scdb_gstat | scdb_gstat - get a gstat data frame. If it is missing and the... |
| scdb_init | Initializing scdb |
| scdb_is_valid | Testing is scdb is initialized |
| scdb_ls | List all object of a given type from the current scdb |
| scdb_ls_loaded | scdb_ls_loaded - list loaded object of a certain type |
| scdb_mat | scdb_mat - get matrix from db, load it if needed |
| scdb_mc | scdb_mc - get a mc object |
| scdb_mc2d | scdb_mc2d - get a mc2d object |
| scdb_mcatlas | scdb_mcatlas - get a mcatlas object |
| scdb_mctnetwork | scdb_mctnetwork - get a mctnetwork object |
| scdb_mgraph | scdb_mgraph - get a mgraph object |
| scfigs_dir | Generate a standard figure dir name igven and object and... |
| scfigs_fn | Generate a standard figure name igven and object and figure... |
| scfigs_init | scgfig_set_base - set base directory for metacell figures,... |
| scm_add_mars_facs_data | Adds FACS index sorting data to matrix metadata table |
| scmat_read_scmat_10x | Read a matrix from the output of a 10x run. Batches can be... |
| scmat_read_scmat_10x_custom | Read a custom count matrix from the output of a 10x run.... |
| scm_downsamp | downsampl |
| scm_export_mat_to_sce | Export a mat object (umi matrix and metadata table) to a... |
| scm_gene_stat | Calculate basic statistics on a matrix |
| scm_ignore_cells | Set ignored (i.e. blacklisted) cells |
| scm_ignore_genes | Set ignored (i.e. blacklisted) genes |
| scm_import_sce_to_mat | Import a umi count matrix with metadata per cell from a... |
| scm_merge_mats | Merge multiple single cell matrix object. |
| scm_new_matrix | Constract a tgScMat |
| scm_sub_mat | Extract sub-matrix. This return a matrix object on a subset... |
| scm_which_downsamp_n | Determine recommended downsampling depth. |
| tgCellGraph-class | Cell graph |
| tgCoClust-class | Metacell colustering object |
| tgGeneSets-class | Gene sets interface |
| tgMC2D-class | Meta cell 2d projection |
| tgMCAtlas-class | wrap up an atlas object from mc, mc2d and matrix ids |
| tgMCCov-class | Meta cell cover |
| tgMCManifGraph-class | manifold graph structure over a metacell object |
| tgMCTNetwork-class | temporal netwrok over metacells |
| tgScMat-class | Single cell RNA-seq matrix |
| tgs_cor_graph | wrapping tgs functions to compute balanced graph from a... |
