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Code Tour: guide to codebase (v2)

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Ivo Kwee edited this page May 23, 2023 · 1 revision

[under construction...]

Folders

  • shiny: Main Shiny app code (app.R).

  • shiny/boards: Code for each analysis module (or 'board') of the app. Each board is coded as a Shiny module.

  • shiny/modules: Lower level Shiny modules that are often used in boards.

  • R: Non-shiny R code: algorithms, plotting functions,etc. Code should not include Shiny code. All code should run without GUI. Files are loosely categorized and prefixed with gx-, pgx- upon the expected input object type.

  • build: Some scripts to build supporting databases that are used by OP

  • cache: Cache objects used for speeding up the start

  • data: Contains the binary PGX files. Each PGX contains pre-computed experiment data.

  • docker: Scripts to build the docker image

  • ext: External files and packages needed by OP

  • lib: Built library files, annotation and reference files.

  • logs: Log files

  • scripts: Example scripts to build some PGX files.

Folders

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