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Interactive Analysis with the cellreportR Shiny App

Source: vignettes/shiny-app.Rmd
shiny-app.Rmd

R-CMD-check pkgdown CRAN status Codecov test coverage CRAN downloads CRAN downloads total License: MIT Lifecycle: experimental

The bundled Shiny application exposes the full cellreportR pipeline through seven guided tabs. It is intended for laboratory personnel without an R background.

Launching 

library(cellreportR)
cr_run_app()                             # example data
cr_run_app(experiment = my_cr_exp)       # your own experiment

Tab overview

  1. Import & Design — upload cell and design files, or load the example data.
  2. Quality Control — set morphology thresholds and remove doublets.
  3. Normalization — background subtraction, control-reference or Z-score.
  4. Statistical Analysis — parametric and non-parametric tests at cell or replicate level, with effect sizes and adjusted p-values.
  5. Dose-Response — fit 4PL / 3PL / linear models and read off IC50.
  6. Visualization — interactive gallery covering all 13 plot types.
  7. Report & Export — generate HTML or PDF reports, export tables and figures.

Cross-tab state

The Shiny app keeps a single cr_experiment in reactiveValues(). QC filtering, normalization and analysis all mutate this object so that downstream tabs react automatically.