Introduction

The crisprShiny package allows users to interact with and visualize CRISPR guide RNAs (gRNAs) stored in GuideSet objects via Shiny applications. This is possible either directly with a self-contained app, or as a module within a larger app. This vignette will demonstrate how to use this package to build Shiny applications for GuideSet objects, and how to navigate gRNA annotation within the app.

Shiny apps created using the crisprShiny package require GuideSet objects be constructed and annotated using the crisprDesign package, however, custom mcols may be added to the GuideSet, as shown below. For more information about how to store and annotate CRISPR gRNAs with GuideSet objects, see our crisprVerse tutorials page.

Installation

crisprShiny can be installed from from the Bioconductor devel branch using the following commands in a fresh R session:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("crisprShiny", version="devel")

Creating self-contained Shiny applications

if (interactive()){
    library(crisprShiny)
    data("guideSetExample_basic", package="crisprShiny")
    app <- crisprShiny(guideSetExample_basic)
    shiny::runApp(app)
}

if (interactive()){
    gs <- guideSetExample_basic[1:50]
    
    ## add custom data columns
    library <- c("lib1", "lib2", "lib3", "lib4")
    set.seed(1000)
    values <- round(rnorm(length(gs)), 4)
    mcols(gs)[["values"]] <- values
    library <- sample(library, length(gs), replace=TRUE)
    mcols(gs)[["library"]] <- library
    
    ## create and run app
    app <- crisprShiny(gs, geneModel=txdb_kras)
    shiny::runApp(app)
}

if (interactive()){
    data("guideSetExample_kras", package="crisprShiny")
    app <- crisprShiny(guideSetExample_kras)
    shiny::runApp(app)
}

Customized apps using Shiny modules

The UI and server components of crisprShiny are also available outside of the crisprShiny function to be used as modules within a larger app that, for instance, may allow the user to parse multiple GuideSet objects in a single session. Below is a simple example that allows the user to explore both the basic and fully-annotated GuideSets used above in the same session.

if (interactive()){
    library(shiny)
    
    ui <- function(id){
        fluidPage(
            sidebarLayout(
                sidebarPanel(
                    selectInput(
                        inputId="guideSet_select",
                        label="Select GuideSet",
                        choices=c("simple", "full")
                    )
                ),
                mainPanel(
                    crisprUI(id)
                )
            )
        )
    }
    
    server <- function(id){
        function(input, output, session){
            guideSet_list <- list("simple"=guideSetExample_basic,
                                  "full"=guideSetExample_kras[1:50])
            gs <- reactive({
                req(input$guideSet_select)
                guideSet_list[[input$guideSet_select]]
            })
            observeEvent(gs(), {
                crisprServer(
                    id,
                    guideSet=gs(),
                    geneModel=txdb_kras,
                    useFilterPresets=TRUE
                )
            })
        }
    }
    
    
    myApp <- function(){
        id <- "id"
        shinyApp(ui=ui(id), server=server(id))
    }
    
    myApp()
}

Session Info

sessionInfo()

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.35.0
## 
## loaded via a namespace (and not attached):
##  [1] cli_3.6.3           knitr_1.49          rlang_1.1.4        
##  [4] xfun_0.49           promises_1.3.2      shiny_1.10.0       
##  [7] xtable_1.8-4        jsonlite_1.8.9      buildtools_1.0.0   
## [10] htmltools_0.5.8.1   maketools_1.3.1     httpuv_1.6.15      
## [13] sys_3.4.3           sass_0.4.9          rmarkdown_2.29     
## [16] evaluate_1.0.1      jquerylib_0.1.4     fontawesome_0.5.3  
## [19] fastmap_1.2.0       yaml_2.3.10         lifecycle_1.0.4    
## [22] BiocManager_1.30.25 compiler_4.4.2      Rcpp_1.0.13-1      
## [25] later_1.4.1         digest_0.6.37       R6_2.5.1           
## [28] magrittr_2.0.3      bslib_0.8.0         tools_4.4.2        
## [31] mime_0.12           cachem_1.1.0