API for espors/idepGolem
Integrated Differential Expression and Pathway Analysis
| Global functions | |
|---|---|
| MDS_plot | Man page Source code |
| PCA_Scree | Man page Source code |
| PCA_biplot | Man page Source code |
| PCA_plot | Man page Source code |
| PCA_plot_3d | Man page Source code |
| PCAtools_eigencorplot | Man page Source code |
| add_legend | Man page Source code |
| app_server | Source code |
| app_sys | Source code |
| app_ui | Source code |
| background_pathway_sets | Man page Source code |
| basic_heat_sub | Man page Source code |
| basic_heatmap | Man page Source code |
| bicluster_summary_message | Man page Source code |
| build_pathway_query | Man page Source code |
| change_names | Man page Source code |
| check_object_state | Man page Source code |
| chr_counts_ggplot | Man page Source code |
| chr_normalized_ggplot | Man page Source code |
| chromosome_plotly | Man page Source code |
| clean_gene_set | Man page Source code |
| clean_query | Man page Source code |
| cluster_heat_click_info | Man page Source code |
| colorpanel2 | Man page Source code |
| connect_convert_db | Man page Source code |
| connect_convert_db_org | Man page Source code |
| conversion_counts_message | Man page Source code |
| convert_data | Man page Source code |
| convert_ensembl_to_entrez | Man page Source code |
| convert_id | Man page Source code |
| cor_plot | Man page Source code |
| counts_bias_message | Man page Source code |
| data_frame_with_list | Man page Source code Source code |
| deg_click_info | Man page Source code |
| deg_deseq2 | Man page Source code |
| deg_heat_data | Man page Source code |
| deg_heat_sub | Man page Source code |
| deg_heatmap | Man page Source code |
| deg_information | Man page Source code |
| deg_limma | Man page Source code |
| detect_groups | Man page Source code |
| dist_functions | Man page Source code |
| doc_hist | Man page Source code |
| draw_sample_tree | Man page Source code |
| dynamic_range | Man page Source code |
| eda_boxplot | Man page Source code |
| eda_density | Man page Source code |
| eda_scatter | Man page Source code |
| enrich_barplot | Man page Source code |
| enrich_net | Man page Source code |
| enrichment_network | Man page Source code |
| enrichment_tree_plot | Man page Source code |
| experiment_design_txt | Man page Source code |
| extract_fcfdr | Man page Source code |
| extract_under | Man page Source code |
| extract_word | Man page Source code |
| fct_01_load_data.R | Man page |
| fct_02_pre_process.R | Man page |
| fct_03_heatmap.R | Man page |
| fct_05_pca.R | Man page |
| fct_06_deg1.R | Man page |
| fct_06_pathway.R | Man page |
| fct_07_genome.R | Man page |
| fct_08_bicluster.R | Man page |
| fct_analysis_random.R | Man page |
| fct_database.R | Man page |
| fgsea_data | Man page Source code |
| find_contrast_samples | Man page Source code |
| find_id_type_by_id | Man page Source code |
| find_overlap | Man page Source code |
| find_overlap_gmt | Man page Source code |
| find_species_by_id | Man page Source code |
| find_species_by_id_name | Man page Source code |
| find_species_id_by_ensembl | Man page Source code |
| gage_data | Man page Source code |
| gene_counts_ggplot | Man page Source code |
| gene_info | Man page Source code |
| generate_colors | Man page Source code |
| generate_descr | Man page Source code |
| genes_stat_table | Man page Source code |
| get_all_gene_names | Man page Source code |
| get_biclust_table_data | Man page Source code |
| get_biclustering | Man page Source code |
| get_gene_info | Man page Source code |
| get_golem_config | Source code |
| get_gsva_plot_data | Man page Source code |
| get_idep_data | Man page Source code |
| get_module_plot | Man page Source code |
| get_network | Man page Source code |
| get_network_plot | Man page Source code |
| get_pathway_list_data | Man page Source code |
| get_pc | Man page Source code |
| get_pc_variance | Man page Source code |
| get_pgsea_plot_all_samples_data | Man page Source code |
| get_pgsea_plot_data | Man page Source code |
| get_plot_height | Man page Source code |
| get_plot_width | Man page Source code |
| get_wgcna | Man page Source code |
| get_wgcna_modules | Man page Source code |
| gg_color_hue | Man page Source code |
| gmt_category | Man page Source code |
| golem_add_external_resources | Source code |
| gsva_data | Man page Source code |
| hcluster_functions | Man page Source code |
| heat_click_info | Man page Source code |
| heat_sub | Man page Source code |
| heatmap_main | Man page Source code |
| hyperText | Man page Source code |
| individual_plots | Man page Source code |
| input_data | Man page Source code |
| k_means_elbow | Man page Source code |
| kegg_pathway | Man page Source code |
| limma_value | Man page Source code |
| list_block_factors_ui | Man page Source code |
| list_comp_venn | Man page Source code |
| list_factors_ui | Man page Source code |
| list_interaction_terms_ui | Man page Source code |
| list_model_comparisons_ui | Man page Source code |
| loose_rock_proper | Man page Source code |
| make_pull_down_menu | Man page Source code |
| max_fun | Man page Source code |
| mean_fun | Man page Source code |
| mean_sd_plot | Man page Source code |
| median_fun | Man page Source code |
| merge_data | Man page Source code |
| mod_01_load_data_server | Source code |
| mod_01_load_data_ui | Source code |
| mod_02_pre_process_server | Source code |
| mod_02_pre_process_ui | Source code |
| mod_03_clustering_server | Source code |
| mod_03_clustering_ui | Source code |
| mod_04_pca_server | Source code |
| mod_04_pca_ui | Source code |
| mod_05_deg_1_ui | Source code |
| mod_05_deg_2_ui | Source code |
| mod_05_deg_server | Source code |
| mod_06_pathway_server | Source code |
| mod_06_pathway_ui | Source code |
| mod_07_genome_server | Source code |
| mod_07_genome_ui | Source code |
| mod_08_bicluster_server | Source code |
| mod_08_bicluster_ui | Source code |
| mod_09_network_server | Source code |
| mod_09_network_ui | Source code |
| mod_10_doc_server | Source code |
| mod_10_doc_ui | Source code |
| mod_11_enrichment_server | Source code |
| mod_11_enrichment_ui | Source code |
| mod_12_heatmap_server | Source code |
| mod_12_heatmap_ui | Source code |
| mod_label_server | Man page Source code |
| mod_label_ui | Man page Source code |
| network_data | Man page Source code |
| network_enrich_data | Man page Source code |
| pathview.stamp | Man page Source code |
| pathway_select_data | Man page Source code |
| pathway_source_info | Man page Source code |
| pc_factor_correlation | Man page Source code |
| pgsea_data | Man page Source code |
| pgsea_plot_all | Man page Source code |
| plot_deg_scatter | Man page Source code |
| plot_gsva | Man page Source code |
| plot_ma | Man page Source code |
| plot_mean_connectivity | Man page Source code |
| plot_pgsea | Man page Source code |
| plot_scale_independence | Man page Source code |
| plot_upset | Man page Source code |
| plot_venn | Man page Source code |
| plot_volcano | Man page Source code |
| pre_process | Man page Source code |
| prep_download | Man page Source code |
| prep_venn | Man page Source code |
| prepare_module_csv | Man page Source code |
| prepare_module_csv_filter | Man page Source code |
| print_dataframe | Man page Source code |
| print_vector | Man page Source code |
| process_heatmap_data | Man page Source code |
| proper | Man page Source code |
| rRNA_counts_ggplot | Man page Source code |
| reactome_data | Man page Source code |
| read_gene_sets | Man page Source code |
| read_gmt | Man page Source code |
| read_gmt_robust | Man page Source code |
| read_pathway_sets | Man page Source code |
| refine_ggplot2 | Man page Source code |
| remove_pathway_id | Man page Source code |
| remove_pathway_id_second | Man page Source code |
| render.kegg.node | Man page Source code |
| rowname_id_swap | Man page Source code |
| run_app | Man page Source code |
| safe_numeric_conversion | Source code |
| sd_density | Man page Source code |
| select_reference_levels_ui | Man page Source code |
| showGeneIDs | Man page Source code |
| sig_genes_plot | Man page Source code |
| sub_heat_ann | Man page Source code |
| sum_fun | Man page Source code |
| t_SNE_plot | Man page Source code |
| total_counts_ggplot | Man page Source code |
| transform_comparisons | Man page Source code |
| utils_analysis_random.R | Man page |
| utils_ui.R | Man page |
| vis_network_plot | Man page Source code |
| volcano_data | Man page Source code |
| wrap_strings | Man page Source code |
