Files in espors/idepGolem
Integrated Differential Expression and Pathway Analysis
.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.gitignore
.lintr
DESCRIPTION
NAMESPACE
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
idepGolem.Rproj
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
inst/app/www/favicon.png
inst/app/www/figs.gif
inst/app/www/flowchart.png
inst/app/www/format.html
inst/app/www/google_analytics_GA4.html
inst/app/www/google_analytics_golem.html
inst/app/www/help_preprocess.html
inst/app/www/idep_logo.png
inst/app/www/messages.html
inst/app/www/pathway.html
inst/golem-config.yml
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/.gitignore
vignettes/Clustering.Rmd
vignettes/Enrichment.Rmd
vignettes/Load_Data.Rmd
vignettes/Pre_Process.Rmd
vignettes/flowchart.png
vignettes/idep_Workflow.Rmd
