Man pages for dputhier/scigenex
The scigenex package (Single-Cell Informative GENe Explorer)
| check_format_cluster_set | Check the format of a Clusterset object |
| ClusterSet-class | ClusterSet-class |
| cluster_set_from_matrix | Transform any matrix and list into a ClusterSet object. |
| cluster_set_from_seurat | Transform a Seurat objects / FindAllMarkers result into a... |
| cluster_set_report | Create a report from a ClusterSet and Seurat object. |
| cluster_set_to_xls | Write Cluster-Set gene lists into an excel sheet. |
| cluster_set_to_xls-ClusterSet-method | Write Cluster-Set gene lists into an excel sheet. |
| cluster_stats | Compute statistics about the clusters |
| cluster_stats-ClusterSet-method | Compute statistics about the clusters |
| clust_names | Names of gene clusters stored in the ClusterSet object |
| clust_names-ClusterSet-method | The names of the gene clusters stored in the ClusterSet... |
| clust_size | Sizes of the clusters stored in a ClusterSet object... |
| clust_size-ClusterSet-method | Sizes of the clusters stored in a ClusterSet object... |
| col_names | Column names of an object |
| col_names-ClusterSet-method | Column names of a ClusterSet object. |
| colors_for_gradient | Generate a vector of colors for a gradient |
| compare_genesets | Compare two lists of gene sets |
| complex9 | The Complex9 dataset A set of 2D points corresponding to 9... |
| complex9Noisy | The complex9Noisy dataset A noisy version of the complex9... |
| construct_new_graph | Construct a new graph for a ClusterSet object |
| create_3_rnd_clust | Generate an example dataset with three clusters of profiles |
| create_4_rnd_clust | Generate an example dataset with four clusters of profiles |
| create_rand_str | Generate a random string of letters and numbers |
| dim-ClusterSet-method | Dimension of a ClusterSet object. dim |
| discrete_palette | Generate a discrete color palette |
| display_hull | Draw a hull around a region of interest of Visium data. |
| enrich_go | Enrichment analysis using GO database of gene clusters from a... |
| enrich_go-ClusterSet-method | Enrichment analysis using GO database of gene clusters from a... |
| filter_by_dot_prod | Filter cluster from a ClusterSet object using dot product. |
| filter_cluster_sd | Filter out gene clusters with small standard deviation. |
| filter_cluster_size | Filter out gene clusters containing few genes |
| filter_nb_supporting_cells | Filter out cluster supported by few cells. |
| gene_cluster | The gene clusters stored in a ClusterSet. gene_cluster |
| gene_cluster-ClusterSet-method | The gene clusters stored in a ClusterSet. gene_cluster |
| gene_clustering | Gene clustering using the Markov Cluster Algorithm (MCL)... |
| get_data_for_scigenex | Fetch an expression matrix from a file, dataframe or Seurat... |
| getFlippedTissueCoordinates | Seurat object internally store spot coordinates (see... |
| get_genes | Extract genes list from each gene clusters. |
| get_verbosity | Get the current verbosity level. |
| grapes-in-grapes-character-ClusterSet-method | Match operator of a ClusterSet object |
| grep_clust | Search genes within ClusterSet using a REGEXP. |
| grep_clust-ClusterSet-method | Search genes within ClusterSet using a REGEXP. |
| install_mcl | Install MCL |
| keep_dbf_graph | Construct a graph based on selected genes in a ClusterSet... |
| load_example_dataset | Load/download a Seurat or ClusterSet example dataset. |
| lymph_node_selected_spot | The lymph_node_selected_spot dataset |
| lymph_node_selected_spot_2 | The lymph_node_selected_spot dataset (#2) |
| mcl_system_cmd | Call MCL program for graph partitioning (internal). |
| module_quality_scores | Compute Gene Module Quality Scores |
| module_quality_scores-ClusterSet-method | Compute Gene Module Quality Scores |
| nclust | Number of clusters in a ClusterSet object. nclust |
| nclust-ClusterSet-method | Number of clusters in a ClusterSet object. nclust |
| ncol.ClusterSet | ncol.ClusterSet |
| nrow.ClusterSet | nrow.ClusterSet |
| plot_clust_enrichments | Plot Cluster Enrichments |
| plot_clust_enrichments-ClusterSet-method | Plot Cluster Enrichments |
| plot_cluster_stats | Plot the result of cluster_stats() |
| plot_cmp_genesets | Plot the result of compare_genesets |
| plot_dist | Plot Distribution of distances |
| plot_ggheatmap | Heatmap of data contained in a ClusterSet object. |
| plot_ggheatmap-ClusterSet-method | Heatmap of data contained in a ClusterSet object. |
| plot_heatmap | plot_heatmap |
| plot_markers_to_clusters | Map cell markers to clusters (hypergeometric/jaccard) |
| plot_markers_to_clusters-ClusterSet-method | Map cell markers to clusters (hypergeometric/jaccard) |
| plot_profiles | Plot mean expression profiles of each cluster from a... |
| plot_spatial | XY scatter plot of Visium data with hexagonal spots. |
| plot_spatial_panel | A planel of XY scatter plots of Visium data with hexagonal... |
| plot_stratum | Display the results of stratify_seurat |
| print_msg | Print a message based on the level of verbosity |
| print_stat | Debugging statistics (vector, matrix or dataframe) |
| rename_clust | Rename the gene clusters of a ClusterSet |
| rename_clust-ClusterSet-method | Rename the gene clusters of a ClusterSet |
| reorder_clust | Reorder the clusters from a ClusterSet |
| reorder_clust-ClusterSet-method | Reorder the clusters from a ClusterSet |
| reorder_genes | Reorder genes in a ClusterSet object. |
| reorder_genes-ClusterSet-method | Reorder genes in a ClusterSet object. |
| row_names | Row names of a ClusterSet object. row_names |
| row_names-ClusterSet-method | Row names of a ClusterSet object. row_names |
| select_genes | Selects informative genes based on k-nearest neighbour... |
| set_verbosity | Set the verbosity level for the SciGeneX package |
| show-ClusterSet-method | The show method of a ClusterSet. |
| show_methods | List the method for the ClusterSet object. |
| stratify_seurat | Given two spot groups, compute for each spot: (i) the... |
| sub-ClusterSet-ANY-ANY-ANY-method | Subsetting operator of a ClusterSet object Extract |
| top_by_go | Select top_genes based on go terms |
| top_by_go-ClusterSet-method | Select top_genes based on go terms |
| top_genes | Most co-expressed genes from each gene cluster |
| top_genes-ClusterSet-method | Most co-expressed genes from each gene cluster |
| viz_enrich | Visualization of enrichment analyses results from a... |
| viz_enrich-ClusterSet-method | Visualization of enrichment analyses results from a... |
| which_clust | Which clusters contain a set of genes. |
| which_clust-ClusterSet-method | Which clusters contain a set of genes. |
