Files in espors/idepGolem

Integrated Differential Expression and Pathway Analysis

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md R/_disable_autoload.R R/app_config.R R/app_server.R R/app_ui.R R/fct_01_load_data.R R/fct_02_pre_process.R R/fct_03_clustering.R R/fct_04_pca.R R/fct_05_deg.R R/fct_06_pathway.R R/fct_07_genome.R R/fct_08_bicluster.R R/fct_09_network.R R/fct_10_doc.R R/fct_11_enrichment.R R/fct_12_heatmap.R R/fct_analysis_random.R R/fct_database.R R/mod_01_load_data.R R/mod_02_pre_process.R R/mod_03_clustering.R R/mod_04_pca.R R/mod_05_deg.R R/mod_06_pathway.R R/mod_07_genome.R R/mod_08_bicluster.R R/mod_09_network.R R/mod_10_doc.R R/mod_11_enrichment.R R/mod_12_heatmap.R R/run_app.R R/utils_analysis_random.R R/utils_ui.R README.md app.R dev/01_start.R dev/02_dev.R dev/03_deploy.R dev/run_dev.R inst/app/www/RMD/clustering_workflow.Rmd inst/app/www/RMD/pathway_workflow.Rmd inst/app/www/RMD/pca_workflow.Rmd inst/app/www/RMD/pre_process_workflow.Rmd inst/app/www/RMD/test_workflow.Rmd man/MDS_plot.Rd man/PCA_Scree.Rd man/PCA_biplot.Rd man/PCA_plot.Rd man/PCA_plot_3d.Rd man/PCAtools_eigencorplot.Rd man/add_legend.Rd man/background_pathway_sets.Rd man/basic_heat_sub.Rd man/basic_heatmap.Rd man/bicluster_summary_message.Rd man/build_pathway_query.Rd man/change_names.Rd man/check_object_state.Rd man/chr_counts_ggplot.Rd man/chr_normalized_ggplot.Rd man/chromosome_plotly.Rd man/clean_gene_set.Rd man/clean_query.Rd man/cluster_heat_click_info.Rd man/colorpanel2.Rd man/connect_convert_db.Rd man/connect_convert_db_org.Rd man/conversion_counts_message.Rd man/convert_data.Rd man/convert_ensembl_to_entrez.Rd man/convert_id.Rd man/cor_plot.Rd man/counts_bias_message.Rd man/data_frame_with_list.Rd man/deg_click_info.Rd man/deg_deseq2.Rd man/deg_heat_data.Rd man/deg_heat_sub.Rd man/deg_heatmap.Rd man/deg_information.Rd man/deg_limma.Rd man/detect_groups.Rd man/dist_functions.Rd man/doc_hist.Rd man/draw_sample_tree.Rd man/dynamic_range.Rd man/eda_boxplot.Rd man/eda_density.Rd man/eda_scatter.Rd man/enrich_barplot.Rd man/enrich_net.Rd man/enrichment_network.Rd man/enrichment_tree_plot.Rd man/experiment_design_txt.Rd man/extract_fcfdr.Rd man/extract_under.Rd man/extract_word.Rd man/fct_01_load_data.R.Rd man/fct_02_pre_process.R.Rd man/fct_03_heatmap.R.Rd man/fct_05_pca.R.Rd man/fct_06_deg1.R.Rd man/fct_06_pathway.R.Rd man/fct_07_genome.R.Rd man/fct_08_bicluster.R.Rd man/fct_analysis_random.R.Rd man/fct_database.R.Rd man/fgsea_data.Rd man/find_contrast_samples.Rd man/find_id_type_by_id.Rd man/find_overlap.Rd man/find_overlap_gmt.Rd man/find_species_by_id.Rd man/find_species_by_id_name.Rd man/find_species_id_by_ensembl.Rd man/gage_data.Rd man/gene_counts_ggplot.Rd man/gene_info.Rd man/generate_colors.Rd man/generate_descr.Rd man/genes_stat_table.Rd man/get_all_gene_names.Rd man/get_biclust_table_data.Rd man/get_biclustering.Rd man/get_gene_info.Rd man/get_gsva_plot_data.Rd man/get_idep_data.Rd man/get_module_plot.Rd man/get_network.Rd man/get_network_plot.Rd man/get_pathway_list_data.Rd man/get_pc.Rd man/get_pc_variance.Rd man/get_pgsea_plot_all_samples_data.Rd man/get_pgsea_plot_data.Rd man/get_plot_height.Rd man/get_plot_width.Rd man/get_wgcna.Rd man/get_wgcna_modules.Rd man/gg_color_hue.Rd man/gmt_category.Rd man/gsva_data.Rd man/hcluster_functions.Rd man/heat_click_info.Rd man/heat_sub.Rd man/heatmap_main.Rd man/hyperText.Rd man/individual_plots.Rd man/input_data.Rd man/k_means_elbow.Rd man/kegg_pathway.Rd man/limma_value.Rd man/list_block_factors_ui.Rd man/list_comp_venn.Rd man/list_factors_ui.Rd man/list_interaction_terms_ui.Rd man/list_model_comparisons_ui.Rd man/loose_rock_proper.Rd man/make_pull_down_menu.Rd man/max_fun.Rd man/mean_fun.Rd man/mean_sd_plot.Rd man/median_fun.Rd man/merge_data.Rd man/mod_label_server.Rd man/mod_label_ui.Rd man/network_data.Rd man/network_enrich_data.Rd man/pathview.stamp.Rd man/pathway_select_data.Rd man/pathway_source_info.Rd man/pc_factor_correlation.Rd man/pgsea_data.Rd man/pgsea_plot_all.Rd man/plot_deg_scatter.Rd man/plot_gsva.Rd man/plot_ma.Rd man/plot_mean_connectivity.Rd man/plot_pgsea.Rd man/plot_scale_independence.Rd man/plot_upset.Rd man/plot_venn.Rd man/plot_volcano.Rd man/pre_process.Rd man/prep_download.Rd man/prep_venn.Rd man/prepare_module_csv.Rd man/prepare_module_csv_filter.Rd man/print_dataframe.Rd man/print_vector.Rd man/process_heatmap_data.Rd man/proper.Rd man/rRNA_counts_ggplot.Rd man/reactome_data.Rd man/read_gene_sets.Rd man/read_gmt.Rd man/read_gmt_robust.Rd man/read_pathway_sets.Rd man/refine_ggplot2.Rd man/remove_pathway_id.Rd man/remove_pathway_id_second.Rd man/render.kegg.node.Rd man/rowname_id_swap.Rd man/run_app.Rd man/sd_density.Rd man/select_reference_levels_ui.Rd man/showGeneIDs.Rd man/sig_genes_plot.Rd man/sub_heat_ann.Rd man/sum_fun.Rd man/t_SNE_plot.Rd man/total_counts_ggplot.Rd man/transform_comparisons.Rd man/utils_analysis_random.R.Rd man/utils_ui.R.Rd man/vis_network_plot.Rd man/volcano_data.Rd man/wrap_strings.Rd tests/testthat.R tests/testthat/test-fct_04_pca.R vignettes/Clustering.Rmd vignettes/Enrichment.Rmd vignettes/Load_Data.Rmd vignettes/Pre_Process.Rmd vignettes/idep_Workflow.Rmd