scharywe/lfapp

The repository includes the development version of R package LFApp

  Shiny Apps for Lateral Flow Assays

The repository includes the development version of R package LFApp

Description

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

(1) LFA App core for image acquisition, editing, region of interest definition via gridding, background correction with multiple available methods, as well as intensity data extraction of the pre-defined bands of the analysed LFAs. More precisely, it consists of Tab 1, Tab 2 and parts of Tab 3 described in detail below.

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

(3) LFA App quantification enables quantification of the extracted intensity values via loading existing calibration models. It extends the LFA App core by Tab 7 described below.

(4) LFA App analysis includes the full functionality mentioned above and enables 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 into several tabs, where each tab represents a specific step of the workflow. While the applications can be used in a sequential fashion, the specific steps can also be carried out individually.

Testing our apps: shinyapps.io

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

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

The mobile version is at

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

Installation

The package requires Bioconductor package EBImage, which should be installed first via

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

Our package depends on the most recent version of package shinyMobile, which must be installed from github (https://github.com/RinteRface/shinyMobile) by

## Install package remotes
if(!requireNamespace("remotes", quietly = TRUE)) 
  install.packages("remotes")
## Install package shinyMobile
remotes::install_github("RinteRface/shinyMobile")

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

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

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

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

Start Apps

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

## desktop versions
## LFA App core
LFApp::run_core()

## LFA App quantification
LFApp::run_quan()

## LFA App calibration
LFApp::run_cal()

## LFA App full analysis
LFApp::run_analysis()

## mobile versions
## LFA App core
LFApp::run_mobile_core()

## LFA App quantification
LFApp::run_mobile_quan()

## LFA App calibration
LFApp::run_mobile_cal()

## LFA App full analysis
LFApp::run_mobile_analysis()

Open User's Guide

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

vignette("LFApp")

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

YouTube Videos

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