Introduction | Installation | Glossary | PipelineTemplate | PipelineDemo | General overview of MagellanNTK | Data format | Modules in MagellanNTK | History | Folder and files configuration | config.txt | General settings | Generic functions | Other informations | R | md | Code Structure of a Shiny Module for MagellanNTK | PipelineName.R file | PipelineName_conf() | PipelineName_ui() and PipelineName_server() | PipelineName_Description.R file | PipelineName_Description_conf() | PipelineName_Description_ui() and PipelineName_Description_server() | PipelineName_Description_server() detailled explanation | PipelineName_Process1.R and PipelineName_Process2.R files | PipelineName_Process1_conf() | PipelineName_Process1_ui() and PipelineName_Process1_server() | PipelineName_Process1_server() detailled explanation | PipelineName_Process1_server() Description sub-step | PipelineName_Process1_server() Sub-step 1 sub-step | PipelineName_Process1_server() Save sub-step | PipelineName_Save.R file | PipelineName_Save_conf() | PipelineName_Save_ui() and PipelineName_Save_server() | PipelineName_Save_server() detailled explanation | PipelineName_Convert.R file | PipelineName_Convert_conf() | PipelineName_Convert_ui() and PipelineName_Convert_server() | PipelineName_Convert_server() detailled explanation | PipelineName_Convert_server() Description sub-step | PipelineName_Convert_server() Convert sub-step 1 sub-step | PipelineName_Convert_server() Save sub-step | Launch the pipeline | Session information
Package: MagellanNTK 0.99.34
Manon Gaudin
MagellanNTK: Configurable Shiny data-analysis workflows
MagellanNTK (Magellan Navigation ToolKit) is a collection of Shiny modules which provide the basis for a generic workflow manager for data processing tools with several steps. It works in combination with any package which implements data processing pipelines compliant with MagellanNTK such as Prostar2.
Authors:
MagellanNTK_0.99.34.tar.gz
MagellanNTK_0.99.34.zip(r-4.7-any)MagellanNTK_0.99.34.zip(r-4.6-any)MagellanNTK_0.99.34.zip(r-4.5-any)
MagellanNTK_0.99.34.tgz(r-4.6-any)MagellanNTK_0.99.34.tgz(r-4.5-any)
MagellanNTK_0.99.34.tar.gz(r-4.7-any)MagellanNTK_0.99.34.tar.gz(r-4.6-any)
MagellanNTK_0.99.34.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MagellanNTK/json (API)
| # Install 'MagellanNTK' in R: |
| install.packages('MagellanNTK', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/edyp-lab/magellanntk/issues
Pkgdown/docs site:https://edyp-lab.github.io
Datasets:
softwareguishinyappsworkflowstep
Last updated from:36b4372d3b. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 197 | ||
| linux-devel | OK | 351 | ||
| source / vignettes | OK | 276 | ||
| linux-release | OK | 317 | ||
| macos-release | OK | 266 | ||
| macos-oldrel | OK | 205 | ||
| windows-devel | OK | 305 | ||
| windows-release | OK | 276 | ||
| windows-oldrel | OK | 291 | ||
| wasm-release | OK | 151 |
Exports:%AND%Add2HistoryaddDatasetsAdditionnalCodeForExternalModulesBuildData2Sendcall_funcchoose_dirConfigdefault_base_URLdefault_funcsdefault_layoutdefault_posdefault_themedefault_workflowdirectoryInputDiscover_Skipped_Stepsdownload_datasetdownload_dataset_serverdownload_dataset_uifile_sepformat_DTformat_DT_serverformat_DT_uiGet_AdditionalModule_Core_CodeGet_Code_Declare_rv_customGet_Code_Declare_widgetsGet_Code_for_dataOutGet_Code_for_General_observeEventsGet_Code_for_ObserveEvent_widgetsGet_Code_for_remoteResetGet_Code_for_resetting_customGet_Code_for_resetting_widgetsGet_Code_for_rv_reactiveValuesGet_Code_Update_Config_VariableGet_Workflow_Core_CodeGetExtensionGetFirstMandatoryNotValidatedGetHistoryGetListDatasetsGetMaxValidated_AllStepsGetMaxValidated_BeforePosGetPackageVersionhistory_datasethistory_dataset_serverhistory_dataset_uiinfos_datasetinfos_dataset_serverinfos_dataset_uiinitCompleteInitializeHistoryInsert_Call_to_Configinsert_mdinsert_md_serverinsert_md_uiInsert_User_SidebarisSubstrkeepDatasetslistBrewerPalettesMagellanNTKMagellanNTK_serverMagellanNTK_uimainappmainapp_servermainapp_uimod_errorModalmod_errorModal_servermod_errorModal_uimod_homepagemod_homepage_servermod_homepage_uimod_modalDialogmod_modalDialog_servermod_modalDialog_uimod_popover_for_helpmod_popover_for_help_servermod_popover_for_help_uimod_release_notesmod_release_notes_servermod_release_notes_uimod_SweetAlertmod_SweetAlert_servermod_SweetAlert_uimodule_existsModule_Return_Funcnav_pipelinenav_pipeline_servernav_pipeline_uinav_processnav_process_servernav_process_uinav_single_processnav_single_process_servernav_single_process_uiNavPageopen_datasetopen_dataset_serveropen_dataset_uiopen_workflowopen_workflow_serveropen_workflow_uipkgsRequireprocess_layoutprocess_layout_pipelineprocess_layout_processreadConfigFilereadDirectoryInputrunDirinputExampleSetCurrentPositionSetHistorysource_shinyApp_filessource_wf_filesstepStatustimeline_pipelinetimeline_pipeline_servertimeline_pipeline_uitimeline_processtimeline_process_servertimeline_process_uiTimestamptl_v_next_iconToggleState_NavBtnsToggleState_ScreenstoggleWidgetUpdate_State_ScreensupdateDirectoryInputUpdateStepsStatusview_datasetview_dataset_serverview_dataset_ui
Dependencies:abindaskpassbase64encBiobaseBiocBaseUtilsBiocGenericsbs4Dashbslibcachemclicommonmarkcpp11crayoncrosstalkcurlDelayedArraydigestdplyrDTevaluatefastmapfontawesomefreshfsgenericsGenomicRangesgluehighrhtmltoolshtmlwidgetshttpuvhttrIRangesjquerylibjsonliteknitrlaterlatticelazyevallifecyclelitedownmagrittrmarkdownMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslotelpillarpkgconfigpromisespurrrR6rappdirsRcpprlangrmarkdownrstudioapiS4ArraysS4VectorssassSeqinfoshinyshinyEffectsshinyjssourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrswaiterwithrxfunxtableXVectoryaml
Build a pipeline with MagellanNTK
Last update: 2026-09-07
Started: 2026-06-15
PipelineDemo User Manual – a vignette template to accompany data analysis pipelines deployed with MagellanNTK
Introduction | Objectives of the vignette | Intuitive overview of the PipelineDemo app | Installation | MagellanNTK jargon | Objects | Timelines | Navigation | Data format requirements | General user interface | Main sidebar | Main interface | Process sidebar | Workflow header | Content area | Step-by-step discovery of PipelineDemo | Launch the pipeline | Open a dataset | Exploratory Data Analyzer (EDA) | Workflow | 'Description' step | 'DataGeneration' step | 'Preprocessing' step | 'Clustering' step | 'Save' step | Other parts of the pipeline | 'Convert' process | 'Save as' tab | 'Manual', 'FAQ' and 'Release Notes' tabs | Other functionalities | Resetting a step | Running a single process | Session information
Last update: 2026-09-07
Started: 2026-06-15
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get the last validated step before current position. | Add2History |
| Builds a vector of data | BuildData2Send |
| Wrapper to the function `do.call` | call_func |
| Choose a Folder Interactively | %AND% choose_dir choose_dir.darwin choose_dir.linux choose_dir.windows file_sep |
| Config class definition | Config Config-class initialize,Config-method |
| Datasets processing | addDatasets addDatasets,list-method dataset-processing keepDatasets keepDatasets,list-method |
| Default variables used in MagellanNTK | default_base_URL default_funcs default_layout default_theme default_vars default_workflow |
| Directory Selection Control | directoryInput |
| Discover Skipped Steps | Discover_Skipped_Steps |
| dl | download_dataset download_dataset_server download_dataset_ui |
| format_DT_ui and format_DT_server | format_DT format_DT_server format_DT_ui |
| Change the default functions in `MagellanNTK` | generic_mod_open_dataset open_dataset open_dataset_server open_dataset_ui |
| Get file extension | GetExtension |
| Get the first mandatory step not validated | GetFirstMandatoryNotValidated |
| Get the history of an assay | GetHistory |
| Get datasets from packages which owns datasets of a given class | GetListDatasets |
| Get the last validated step | GetMaxValidated_AllSteps |
| Get the last validated step before current position. | GetMaxValidated_BeforePos |
| Get the version of a package installed in the local R distribution | GetPackageVersion |
| Global variables | default_pos globalvariables listBrewerPalettes stepStatus tl_v_next_icon |
| Initialisation function for DT | initComplete |
| Get the last validated step before current position. | InitializeHistory |
| Insert source code for config() | Insert_Call_to_Config |
| R code to update the 'config' variable of a process module | AdditionnalCodeForExternalModules Get_AdditionalModule_Core_Code Get_Code_Declare_rv_custom Get_Code_Declare_widgets Get_Code_for_dataOut Get_Code_for_General_observeEvents Get_Code_for_ObserveEvent_widgets Get_Code_for_remoteReset Get_Code_for_resetting_custom Get_Code_for_resetting_widgets Get_Code_for_rv_reactiveValues Get_Code_Update_Config_Variable Get_Workflow_Core_Code insertCodeForExternalModules Module_Return_Func |
| Substring test | isSubstr |
| lldata dataset | lldata |
| lldata1 dataset | lldata1 |
| lldata12 dataset | lldata12 |
| lldata123 dataset | lldata123 |
| Main Shiny application | MagellanNTK magellanNTK MagellanNTK_server MagellanNTK_ui |
| A modal window to display messages | mod_errorModal mod_errorModal_server mod_errorModal_ui mod_err_modal |
| mod_homepage_ui and mod_homepage_server | mod_homepage mod_homepage_server mod_homepage_ui |
| insert_md_ui and insert_md_server | insert_md insert_md_server insert_md_ui mod_insert_md |
| mod_main_page_ui and mod_loading_page_server | mainapp mainapp_server mainapp_ui mod_main_page |
| Predefined modal with embeded shiny module | mod_modalDialog mod_modalDialog_server mod_modalDialog_ui |
| mod_open_workflow_ui and mod_open_workflow_server | mod_open_workflow open_workflow open_workflow_server open_workflow_ui |
| Opens a small tooltip info over a widget. | mod_popover_for_help mod_popover_for_help_server mod_popover_for_help_ui |
| mod_release_notes_ui and mod_release_notes_server | mod_release_notes mod_release_notes_server mod_release_notes_ui |
| A shiny app to display a modal | mod_SweetAlert mod_sweetAlert mod_SweetAlert_server mod_SweetAlert_ui |
| Checks if a Shiny module is loaded | module_exists |
| Shiny module `nav_pipeline()` | nav_pipeline nav_pipeline_server nav_pipeline_ui |
| The server() function of the module `nav_process` | nav_process nav_process_server nav_process_ui |
| Shiny module `nav_single_process()` | nav_single_process nav_single_process_server nav_single_process_ui |
| Move the position of the cursor | NavPage |
| Loads packages | pkgsRequire |
| Layout for workflows | process_layout process_layout_pipeline process_layout_process |
| Read pipelines configuration files | readConfigFile |
| Read the value of a directoryInput | readDirectoryInput |
| Runs a demo app with the code | runDirinputExample |
| Get the position of the last validated item | SetCurrentPosition |
| Standardize names | SetHistory |
| Prints the content of a `Config` class | show,Config-method |
| Sidebar functions | Insert_User_Sidebar sidebars |
| Source ui.R, server.R ang global.R files | source_shinyApp_files |
| Source workflow files | source_wf_files |
| Shiny module for the process timeline | timelines timeline_pipeline timeline_pipeline_server timeline_pipeline_ui timeline_process timeline_process_server timeline_process_ui |
| Timestamp in UNIX format. | Timestamp |
| Updates the state of navigation buttons | ToggleState_NavBtns |
| Updates the status of steps in a given range | ToggleState_Screens |
| Hide/show a widget w.r.t a condition. | toggleWidget |
| Update the status enabled/disabled of the steps of a pipeline/process | Update_State_Screens |
| Change the value of a directoryInput on the client | updateDirectoryInput |
| Update the status of steps in a pipeline nor process. | UpdateStepsStatus |
| mod_open_demo_dataset_ui and mod_open_demo_dataset_server | view_dataset view_dataset_server view_dataset_ui |