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The repository includes the development version of R package LFApp

The LFA shiny apps include in package LFApp consist of four modular Shinyapplications:

(1)LFA App core for image acquisition, editing, region of interest definitionvia gridding, background correction with multiple available methods, as well asintensity data extraction of the pre-defined bands of the analysed LFAs. Moreprecisely, it consists of Tab 1, Tab 2 and parts of Tab 3 described in detailbelow.

(2)LFA App calibration extends the LFA App core by methods for merging theintensity data with information from experiments, computation of calibrationmodels and the generation of a report about the calibration analysis. Thefunctionality corresponds to the Tabs 1-6 described below.

(3)LFA App quantification enables quantification of the extracted intensityvalues via loading existing calibration models. It extends the LFA App coreby Tab 7 described below.

(4)LFA App analysis includes the full functionality mentioned above andenables full analysis in one application. That is, it consists of Tab 1-7.

The graphical user interface of the apps is built in a modular way divided intoseveral tabs, where each tab represents a specific step of the workflow. Whilethe applications can be used in a sequential fashion, the specific steps canalso be carried out individually.

Our apps can also be tested on shinyapps.io. The desktop version of our fullpurpose analysis app is at

https://lfapp.shinyapps.io/LFAnalysis/

The mobile version is at

https://lfapp.shinyapps.io/mobile_app/

The package requires Bioconductor package EBImage, which should be installedfirst via

## Install package BiocManagerif(!requireNamespace("BiocManager", quietly = TRUE))   install.packages("BiocManager")## Use BiocManager to install EBImageBiocManager::install("EBImage", update = FALSE)

For generating our vignette and automatic reports, we need packages knitr andrmarkdown, which will be installed next.

## Install package knitrif(!requireNamespace("knitr", quietly = TRUE))   install.packages("knitr")## Install package rmarkdownif(!requireNamespace("rmarkdown", quietly = TRUE))   install.packages("rmarkdown")

Finally, one can install package LFApp, where all remaining dependencies willbe installed automatically.

## Install package LFAppremotes::install_github("fpaskali/LFApp", build_vignette=TRUE)

LFApp consist of four different shiny apps where there is a desktop and amobile version for each app. They can be started with one of the followingcommands:

## desktop versions## LFA App coreLFApp::run_core()## LFA App quantificationLFApp::run_quan()## LFA App calibrationLFApp::run_cal()## LFA App full analysisLFApp::run_analysis()## mobile versions## LFA App coreLFApp::run_mobile_core()## LFA App quantificationLFApp::run_mobile_quan()## LFA App calibrationLFApp::run_mobile_cal()## LFA App full analysisLFApp::run_mobile_analysis()

A comprehensive user's guide is included in our package in form of a so-calledvignette and can be opened via

vignette("LFApp")

You can also find it athttps://fpaskali.github.io/LFApp/

There is a playlist athttps://www.youtube.com/playlist?list=PLRgOZXM8LZ0gJwtsFNxBiu9WJG1TJjFuP