├── .gitignore ├── LICENSE ├── README.md ├── Version.md ├── easyGEO ├── bug_report │ └── out_of_ram_report.csv ├── global.R ├── global │ └── functions.R ├── google-analytics.html ├── inc │ ├── data_matrix.tsv │ ├── data_matrix_sample.tsv │ ├── design_matrix.csv │ ├── design_matrix_sample.csv │ ├── easyGEO_example1.rnk │ ├── help_button_page.Rmd │ └── help_button_page.html ├── intro │ ├── D_manual.txt │ ├── D_post.txt │ ├── D_pre.txt │ ├── E_manual.txt │ ├── E_post.txt │ ├── E_post_with_summary_ui.txt │ ├── E_pre.txt │ ├── F_post.txt │ ├── F_pre.txt │ ├── R_post.txt │ ├── R_post_deg.txt │ ├── R_pre.txt │ ├── V_explore.txt │ ├── V_explore_violin.txt │ ├── V_heatmap.txt │ ├── V_pre.txt │ └── V_volcano.txt ├── rvs │ ├── all_samples.rds │ ├── c_level.rds │ ├── c_var.rds │ ├── deg.rds │ ├── deg_counts.rds │ ├── deg_pdata.rds │ ├── dmdf.rds │ ├── fddf.rds │ ├── gpl_choices.rds │ ├── gpl_summary.rds │ ├── gpl_tooltips.rds │ ├── gse_all.rds │ ├── matrix_ready.rds │ ├── pdata.rds │ ├── platforms.rds │ ├── samples.rds │ ├── samples_c.rds │ ├── samples_t.rds │ ├── sup_source.rds │ ├── suplist.rds │ ├── t_level.rds │ └── text.rds ├── rvs2 │ ├── all_samples.rds │ ├── c_level.rds │ ├── c_var.rds │ ├── deg.rds │ ├── deg_counts.rds │ ├── deg_pdata.rds │ ├── dmdf.rds │ ├── dmdf_samples.rds │ ├── fddf.rds │ ├── fddf_o.rds │ ├── gpl_tooltips.rds │ ├── matrix_ready.rds │ ├── pdata.rds │ ├── samples.rds │ ├── samples_c.rds │ ├── samples_t.rds │ ├── sup_source.rds │ ├── suplist.rds │ ├── t_level.rds │ └── text.rds ├── server.R ├── server │ ├── 1.1_load_geo.R │ ├── 1.2_show_metadata.R │ ├── 2.1_design_summary.R │ ├── 2.2_filter_design.R │ ├── 3_data_matrix.R │ ├── 4.1_select_comparison.R │ ├── 4.2_confirm_matrix.R │ ├── 4.3_run_deg.R │ ├── 5_vis.R │ ├── DE.R │ ├── demo.R │ ├── functions.R │ ├── help.R │ ├── rv.R │ ├── server-palettes.R │ ├── server-ramCheck.R │ └── server-variables.R ├── ui.R ├── ui │ └── css_addons.R └── www │ └── style.css ├── easyGSEA ├── bug_report │ └── out_of_ram_report.csv ├── global.R ├── google-analytics.html ├── inc │ ├── bta.csv │ ├── bta.rnk │ ├── cel.csv │ ├── cel.rnk │ ├── cel2_example1.rnk │ ├── cel2_example2.csv │ ├── cfa.csv │ ├── cfa.rnk │ ├── dme.csv │ ├── dme.rnk │ ├── dre.csv │ ├── dre.rnk │ ├── edge_explaination.md │ ├── edge_threshold_explaination.md │ ├── gga.csv │ ├── gga.rnk │ ├── glist_example_genes.csv │ ├── hsa.csv │ ├── hsa.rnk │ ├── mmu.csv │ ├── mmu.rnk │ ├── p_explaination.md │ ├── rnk_explaination.md │ ├── rno.csv │ ├── rno.rnk │ ├── sce.csv │ ├── sce.rnk │ ├── some_words.csv │ ├── ssc.csv │ └── ssc.rnk ├── intro │ ├── D_post.txt │ ├── D_pre.txt │ ├── EN_post.txt │ ├── EN_pre.txt │ ├── ER_post.txt │ ├── ER_post_with_pathway.txt │ ├── ER_pre.txt │ ├── R_post.txt │ ├── R_post_ora.txt │ ├── R_post_with_conversion_table.txt │ ├── R_post_with_conversion_table_ora.txt │ ├── R_pre.txt │ └── R_pre_ora.txt ├── rvs │ ├── bar_pathway.rds │ ├── bubble_pathway.rds │ ├── data_head_o.rds │ ├── db_modal.rds │ ├── db_status.rds │ ├── dbs.rds │ ├── fgseagg.rds │ ├── file_upload_status.rds │ ├── gene_lists.rds │ ├── gene_lists_after.rds │ ├── gene_lists_mat1.rds │ ├── gene_lists_mat2.rds │ ├── glist_check.rds │ ├── gmax.rds │ ├── gmin.rds │ ├── gmt_cs.rds │ ├── gmt_cs_paths.rds │ ├── gmts.rds │ ├── gmts_length.rds │ ├── gperm.rds │ ├── infile_check.rds │ ├── infile_confirm.rds │ ├── infile_name.rds │ ├── infile_path.rds │ ├── no_down_01.rds │ ├── no_down_05.rds │ ├── no_up_01.rds │ ├── no_up_05.rds │ ├── rnk_check.rds │ ├── rnk_or_deg.rds │ ├── rnkgg.rds │ ├── rnkll.rds │ ├── run.rds │ ├── run_mode.rds │ ├── run_n.rds │ ├── sd_high.rds │ ├── total_genes.rds │ ├── total_genes_after.rds │ └── volcano_pathway.rds ├── rvs2 │ ├── bar_pathway.rds │ ├── bubble_pathway.rds │ ├── data_head_o.rds │ ├── db_modal.rds │ ├── db_status.rds │ ├── dbs.rds │ ├── fgseagg.rds │ ├── file_upload_status.rds │ ├── gene_lists.rds │ ├── gene_lists_after.rds │ ├── gene_lists_mat1.rds │ ├── gene_lists_mat2.rds │ ├── glist_check.rds │ ├── gmax.rds │ ├── gmin.rds │ ├── gmt_cs.rds │ ├── gmt_cs_paths.rds │ ├── gmts.rds │ ├── gmts_length.rds │ ├── gperm.rds │ ├── infile_check.rds │ ├── infile_confirm.rds │ ├── infile_name.rds │ ├── no_down_01.rds │ ├── no_down_05.rds │ ├── no_up_01.rds │ ├── no_up_05.rds │ ├── rnk_check.rds │ ├── rnk_or_deg.rds │ ├── rnkgg.rds │ ├── rnkll.rds │ ├── run.rds │ ├── run_mode.rds │ ├── run_n.rds │ ├── sd_high.rds │ └── volcano_pathway.rds ├── server.R ├── server │ ├── 1.1.server-run.R │ ├── 1.2.server-body1.R │ ├── 2.server-results.R │ ├── 3.server-network.R │ ├── 4.server-download.R │ ├── demo.R │ ├── help.R │ ├── server-functions.R │ ├── server-ramCheck.R │ ├── server-reactives.R │ ├── server-rv.R │ └── server-variables.R ├── ui.R ├── ui │ ├── 1.ui-run.R │ ├── 2.ui-results.R │ ├── 3.ui-network.R │ ├── 4.ui-download.R │ ├── 5.ui-help.R │ └── css_addons.R └── www │ ├── demo │ ├── gsea.kegg.png │ ├── hsa.csv │ ├── hsa.rnk │ ├── hsa.zip │ └── hsa_list.txt │ ├── gmt_abbreviations.tsv │ ├── gmts │ ├── ORA │ │ └── cel.csv │ ├── gmts_list.csv │ └── gmts_list_selected.csv │ ├── markdown_picture.jpg │ ├── reactome.js │ ├── style.css │ └── upload.jpg └── easyVizR ├── bug_report └── out_of_ram_report.csv ├── global.R ├── global ├── functions.R └── init.R ├── google-analytics.html ├── inc ├── edge_explaination.md ├── edge_threshold_explaination.md └── upload_q.md ├── intro ├── f0.txt ├── f1.txt ├── i0.txt ├── i1.txt ├── n0.txt ├── n2.txt ├── n3.txt ├── n_RRHO.txt ├── n_correlogram.txt ├── n_nw.txt ├── n_single.txt ├── upload.txt ├── x0.txt └── x1.txt ├── rvs ├── FileDf.rds ├── all_char_stats.rds ├── batch_failed.rds ├── batch_files.rds ├── columnCount.rds ├── detected_dbs.rds ├── df_n.rds ├── folder_upload_state.rds ├── gg.rds ├── gls_text.rds ├── gls_ui.rds ├── heatmap_i.rds ├── heatmap_sortby.rds ├── hm_numeric_stats.rds ├── ins_criteria.rds ├── ins_venn_palette.rds ├── ll.rds ├── n_3ds_status.rds ├── n_css_highlights.rds ├── n_igl.rds ├── n_ins_namelen.rds ├── n_ins_view.rds ├── n_sharedcols.rds ├── n_sharedrows.rds ├── n_to_plot.rds ├── n_ui_showpanel.rds ├── n_venn_status.rds ├── nic.rds ├── nw_char_stats.rds ├── nx_i.rds ├── nx_n.rds ├── opt_easygsea_filter_db.rds ├── s.rds ├── tt.rds ├── upload_batch_colscheme.rds ├── upload_batch_columns.rds ├── upload_batch_sharedcols.rds ├── upload_columns.rds └── v.rds ├── server.R ├── server ├── demo.R ├── f_gls.R ├── functions.R ├── functions_vis.R ├── help.R ├── i_ins.R ├── multi_events.R ├── multi_shared_widgets.R ├── n_ui.R ├── n_vis_correlogram.R ├── n_vis_heatmap.R ├── n_vis_network.R ├── n_vis_rrho.R ├── n_vis_scatter.R ├── n_vis_single.R ├── organize.R ├── rv.R ├── server-init.R ├── server-palettes.R └── server-ramCheck.R ├── ui.R ├── ui ├── body1.R ├── body2.R ├── body3.R ├── body_filters.R ├── body_ins.R ├── css_addons.R ├── sideopt2.R └── sideopt3.R └── www ├── demo.zip ├── getIP.js └── style.css /.gitignore: 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