├── .RData ├── .github └── ISSUE_TEMPLATE │ ├── bug_report-ORHUN.md │ └── bug_report.md ├── .gitignore ├── DO-MS.Rproj ├── LICENSE ├── README.md ├── do-ms_cmd.R ├── docs ├── .gitignore ├── .stylelintrc.json ├── 404.html ├── CNAME ├── Gemfile ├── LICENSE.txt ├── Rakefile ├── _config.yml ├── _includes │ ├── head.html │ └── nav.html ├── _layouts │ ├── about.html │ ├── default.html │ ├── home.html │ ├── page.html │ └── post.html ├── _sass │ ├── base.scss │ ├── buttons.scss │ ├── code.scss │ ├── color_schemes │ │ ├── blue.scss │ │ └── dark.scss │ ├── content.scss │ ├── custom │ │ └── custom.scss │ ├── labels.scss │ ├── layout.scss │ ├── navigation.scss │ ├── search.scss │ ├── support │ │ ├── _functions.scss │ │ ├── _variables.scss │ │ ├── mixins │ │ │ ├── _buttons.scss │ │ │ ├── _layout.scss │ │ │ ├── _typography.scss │ │ │ └── mixins.scss │ │ └── support.scss │ ├── tables.scss │ ├── typography.scss │ ├── utilities │ │ ├── _colors.scss │ │ ├── _layout.scss │ │ ├── _lists.scss │ │ ├── _spacing.scss │ │ ├── _typography.scss │ │ └── utilities.scss │ └── vendor │ │ └── normalize.scss │ │ ├── README.md │ │ ├── normalize.scss │ │ └── package.json ├── assets │ ├── css │ │ ├── dark-mode-preview.scss │ │ └── just-the-docs.scss │ ├── images │ │ ├── TOC_Graphic_noOutline_abstract_v18.png │ │ ├── add_folder_path.png │ │ ├── dia_input.png │ │ ├── do-ms-add-folder-btn.png │ │ ├── do-ms-dia-example.png │ │ ├── do-ms-dia-foldername.png │ │ ├── do-ms-dia-generate-report.png │ │ ├── do-ms-dia-import.png │ │ ├── do-ms-dia-info.png │ │ ├── do-ms-dia-load.png │ │ ├── do-ms-dia-overview.png │ │ ├── do-ms-dia-pathname.png │ │ ├── do-ms-dia-rename.png │ │ ├── do-ms-dia-results.png │ │ ├── do-ms-dia_config.png │ │ ├── do-ms-dia_mode.png │ │ ├── do-ms-dia_title.png │ │ ├── do-ms-dia_title_v2.png │ │ ├── do-ms-enter-path.png │ │ ├── do-ms-osx-folder-info.png │ │ ├── do-ms-osx-path-after.png │ │ ├── do-ms-osx-path-before.png │ │ ├── do-ms-proj.png │ │ ├── do-ms-run.png │ │ ├── do-ms-windows-path-after.png │ │ ├── do-ms-windows-path-before.png │ │ ├── download_data.png │ │ ├── download_image.png │ │ ├── generate_report_Rstudio_progress.png │ │ ├── generate_report_page.png │ │ ├── generate_report_progress.png │ │ ├── import_data_loaded_status.png │ │ ├── import_exp_format.png │ │ ├── import_exp_table.png │ │ ├── import_exp_table_after_format.png │ │ ├── import_exp_table_after_regex.png │ │ ├── import_exp_table_edit.png │ │ ├── import_folder_added.png │ │ ├── import_folder_selected.png │ │ ├── import_load_data.png │ │ ├── import_load_progress.png │ │ ├── import_page_empty.png │ │ ├── import_regex.png │ │ ├── just-the-docs.png │ │ ├── module_help_text.png │ │ ├── module_right_click_image.png │ │ ├── osx_get_path.png │ │ ├── preprocessing_input.png │ │ ├── preprocessing_output.png │ │ ├── report_html.png │ │ ├── search.svg │ │ ├── subset_D_1_to_3.png │ │ ├── subset_apex_offset.png │ │ └── subset_open_menu.png │ └── js │ │ ├── just-the-docs.js │ │ ├── search-data.json │ │ └── vendor │ │ ├── MathJax.js │ │ └── lunr.min.js ├── bin │ └── just-the-docs ├── build_search_index.sh ├── docs │ ├── DO-MS_examples.md │ ├── adding_folders.md │ ├── automation.md │ ├── build_your_own.md │ ├── getting_started.md │ ├── getting_started_app.md │ ├── getting_started_cmd.md │ ├── getting_started_dia_app.md │ ├── getting_started_preprocessing.md │ ├── hosting_as_server.md │ ├── installation.md │ ├── known_issues.md │ ├── other_search_engines.md │ └── session_info.md ├── index.md ├── just-the-docs.gemspec ├── lib │ └── tasks │ │ └── search.rake ├── mass-spec │ └── methods.md ├── package-lock.json ├── package.json ├── script │ └── build └── serve.sh ├── example ├── archived_modules │ ├── 070_DART-ID │ │ ├── dart_00_pep_scatter.R │ │ ├── dart_01_fdr_increase.R │ │ ├── dart_02_alignment.R │ │ ├── dart_03_ids_per_exp.R │ │ ├── dart_04_fractional_ID_rate.R │ │ └── dart_05_total_ID_rate.R │ ├── scope_02_TMT_int.R │ └── scope_03_relative_RI_int.R ├── config_file.yaml ├── config_file_diann.yaml ├── config_sqc68.yaml ├── plot_module.R ├── table_module.R ├── text_module.R └── wip_modules │ └── contam_05_z1z2_duty_cycle.R ├── global.R ├── manuscript └── PlotsForPub.RMD ├── modules ├── dia-nn │ ├── 005_Summary │ │ └── summary_001_experiments.R │ ├── 020_Ion_Sampling │ │ ├── Instrument_11_ms1_fill_time_dist.R │ │ ├── Instrument_12_ms1_tic.R │ │ ├── Instrument_13_ms1_fill_times.R │ │ ├── Instrument_14_ms2_fill_time_dist.R │ │ ├── Instrument_15_ms2_fill_times.R │ │ ├── Instrument_16_ms2_fill_time_matrix.R │ │ ├── instrument_01_DIA_MS1_int_ID_Label.R │ │ ├── instrument_02_IDs_by_RT.R │ │ ├── instrument_03_DIA_MS1_int_ID.R │ │ ├── instrument_04_DIA_MS1_Intersected_int.R │ │ ├── instrument_05_DIA_MS1_Intersected_int_Norm.R │ │ ├── instrument_06_charge_count.R │ │ ├── instrument_07_DIA_MS2_Intersected_int.R │ │ ├── instrument_08_DIA_MS2_Intersected_int_Norm.R │ │ ├── instrument_09_DIA_MS2_vs_MZ.R │ │ ├── instrument_10_DIA_IM_Intersected_int_Norm.R │ │ ├── instrument_16_xic.R │ │ ├── instrument_17_DIA_MS1_counts.R │ │ ├── instrument_18_FragQuant_abs.R │ │ ├── instrument_19_FragQuant_rel.R │ │ └── instrument_20_DIA_MS1_MS2_Ratio.R │ ├── 030_Identifications │ │ ├── 00_PEP_colored_cumulative_update.R │ │ ├── 01_ms1vsms2_IDs.R │ │ ├── 02_modified_IDs.R │ │ ├── 05_miscleavage_table.R │ │ ├── 10_miscleavage_K.R │ │ ├── 10_miscleavage_R.R │ │ └── 20_protein_groups.R │ ├── 040_Chromatography │ │ └── 10_fwhm.R │ ├── 050_plex-DIA_Diagnostics │ │ ├── 20_total_IDs.R │ │ ├── 21_channel_ids.R │ │ ├── 24_protein_IDs.R │ │ ├── 30_channel_intensity.R │ │ ├── 31_quantification_variability_MS1.R │ │ ├── 32_quantification_variability_MS2.R │ │ ├── 40_ms1_ids.R │ │ ├── 50_missing_data_precursor.R │ │ └── 51_missing_data_proteins.R │ └── 060_Feature_Detection │ │ ├── 01_charge_distribution.R │ │ ├── 02_nIsotopes.R │ │ ├── 03_nscans.R │ │ ├── 041_IDs_by_RT.R │ │ ├── 042_IDs_by_mz.R │ │ ├── 04_RT_length_base.R │ │ └── 05_intensity_distribution.R └── max_quant │ ├── 005_Summary │ ├── summary_005_maxquant.R │ ├── summary_010_expmap.R │ ├── summary_020_parameters.R │ └── summary_030_expsummary.R │ ├── 010_Chromatography │ ├── chrom_00_FWHM.R │ ├── chrom_00_FWHM_most_intense.R │ ├── chrom_01_IDfreq_by_RT.R │ └── chrom_02_RT_length_base.R │ ├── 020_Ion_Sampling │ ├── instrument_00_apex_offset.R │ ├── instrument_01_MS1_int_ID.R │ ├── instrument_02_MS1_Intersected_int.R │ ├── instrument_02_MS1_Intersected_int_Norm.R │ ├── instrument_02_MS1_int_z_gt_1.R │ ├── instrument_03_MS1_int_z_all.R │ ├── instrument_04_injection_time_PSM.R │ ├── instrument_04_ms2_per_PSM.R │ ├── instrument_05_injection_time_noPSM.R │ ├── instrument_06_MS1_fill_time.R │ ├── instrument_07_MS1_dutycycle_RT.R │ ├── instrument_09__duty_cycle_IDrate.R │ └── instrument_10_RI_precursor.R │ ├── 030_Peptide_Identifications │ ├── 00_miscleavage.R │ ├── 05_miscleavage_table.R │ ├── 10_PEP_colored_cumulative_update.R │ ├── 25_PIF.R │ ├── 30_fractional_ID_rate.R │ ├── 30_fractional_ID_rate_intensitybins.R │ ├── 40_total_ID_rate.R │ ├── dart_00_a_link2.R │ ├── dart_00_pep_scatter.R │ ├── dart_01_fdr_increase.R │ ├── dart_02_alignment.R │ ├── dart_03_ids_per_exp.R │ ├── dart_04_fractional_ID_rate.R │ └── dart_05_total_ID_rate.R │ ├── 040_Contamination │ ├── contam_00_charge_count.R │ ├── contam_01_charge_tic.R │ ├── contam_02_MS1_int_z_1.R │ ├── contam_03_mz_z_1.R │ ├── contam_04_z1_int_by_RT.R │ └── contam_04_z2_int_by_RT.R │ ├── 050_SCoPE-MS_Diagnostics │ ├── scope_001_med_RI_heatmap.R │ ├── scope_00_NAs.R │ ├── scope_05_misscleavages_sc.R │ ├── scope_07_scRI_swarmplot.R │ ├── scope_08_rRI_vs_RT.R │ ├── scope_09_scRI_swarmplot_cors.R │ ├── scope_11_synthetic_peptides.R │ ├── scope_12_RI_contam.R │ ├── scope_12_a_explain.R │ └── scope_13_cor_mat.R │ └── 080_Carrier │ ├── carrier_00.R │ ├── carrier_01_label_efficiency.R │ ├── carrier_02_RelativeAbundance.R │ ├── carrier_03__miscleavage_table.R │ └── carrier_04_R_vs_K_missedcleavages.R ├── pipeline ├── __init__ ├── env.yml ├── env_loose.yml ├── processing.py ├── requirements.txt └── test_processing.py ├── resources ├── app.css ├── app.js └── inclusion_list_example.csv ├── server.R ├── server ├── build_modules.R └── generate_report.R ├── settings.yaml ├── start_server.R ├── start_server.bat ├── start_server.sh ├── ui.R ├── ui ├── documentation_tab.R ├── import_tab.R ├── report_tab.R └── settings_tab.R └── www └── GitHub_Logo_White.png /.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SlavovLab/DO-MS/HEAD/.RData -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report-ORHUN.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SlavovLab/DO-MS/HEAD/.github/ISSUE_TEMPLATE/bug_report-ORHUN.md 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