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Analyse a screen in the browser with the ScreenR app

Source: R/run_screenr_app.R
run_screenr_app.Rd

Opens an interactive application, built with Shiny, that runs the main steps of a ScreenR analysis without writing code: loading the counts (an example screen, a count table with its annotation, or a MAGeCK count file), describing the samples, quality control, finding the hits with several methods and checking each hit at the level of its barcodes. Tables and plots can be downloaded, together with an R script that repeats the analysis.

The app needs the packages shiny, bslib and DT (install them with BiocManager::install(c("shiny", "bslib", "DT"))).

Usage

run_screenr_app(object = NULL, ...)

screenr_app(object = NULL)

Arguments

object

An optional ScreenR object to open in the app, for example one created with create_screenr_object. If NULL the app starts from the data page.

...

Further arguments passed to runApp, such as launch.browser or port.

Value

run_screenr_app() runs the app and returns when it is closed. screenr_app() returns the app (a shiny.appobj), which can be run with shiny::runApp() or deployed to a Shiny server.

Examples

if (interactive()) {
    run_screenr_app()

    # Open an object that is already in the session
    data(count_table)
    data(annotation_table)
    object <- create_screenr_object(
        table = count_table, annotation = annotation_table,
        groups = factor(c(
            "T1/T2", "T1/T2", "Time3_TRT", "Time3_TRT", "Time3_TRT",
            "Time3_CTRL", "Time3_CTRL", "Time3_CTRL", "Time4_TRT",
            "Time4_TRT", "Time4_TRT", "Time4_CTRL", "Time4_CTRL",
            "Time4_CTRL"
        ))
    )
    run_screenr_app(object)
}