Package 'crisprShiny'

Server component for crisprShiny App

Description

Server component for crisprShiny App. Not intended for direct use. (intended to be passed as server component of module in shinyApp function)

Usage

crisprServer(id, guideSet, geneModel, title = NULL, useFilterPresets = TRUE)

Arguments

id	Module ID.
guideSet	A GuideSet object.
geneModel	A GRangesList object obtained using crisprDesign::TxDb2GRangesList.
title	Optional title to display at head of app.
useFilterPresets	Whether to use preset filter values on app launch. See details section for ?crisprShiny.

Value

Shiny module server component.

Examples

library(crisprShiny)
ui <- function(id){
    fluidPage(
        crisprUI(id)
    )
}

server <- function(id, gs){
    function(input, output, session){
        observeEvent(gs, {
            crisprServer(
                id,
                guideSet=gs,
                geneModel=NULL,
                useFilterPresets=TRUE
            )
        })
    }
}

myApp <- function(gs){
    shinyApp(ui=ui("id"), server=server("id", gs))
}

if (interactive()){
    data("guideSetExample_basic", package="crisprShiny")
    myApp(guideSetExample_basic)
}

---

Interactive visualization of GuideSets via Shiny applications

Description

Means to interactively visualize gRNAs within a GuideSet object via a Shiny application. Contents of the Shiny app reflect annotations contained within the GuideSet object, and provide intuitive controls to examine, filter, and export .csv tables of gRNAs.

Usage

crisprShiny(guideSet, geneModel = NULL, useFilterPresets = TRUE)

Arguments

guideSet	A GuideSet object.
geneModel	A GRangesList object obtained using crisprDesign::TxDb2GRangesList.
useFilterPresets	Whether to use preset filter values on app launch. See details.

Details

Preset filter values

Using sensible, preset filters can conveniently remove many poorer-quality gRNAs from view upon app launch. This can be done by setting useFilterPresets=TRUE, while passing FALSE will retain all gRNAs in guideSet. Of course, filters can still be adjusted within the app to either further refine or broaden the list of gRNAs to view. Setting useFilterPresets=TRUE (default) will impose the following filter criteria, as appropriate to the guideSet, upon app launch:

• spacers with polyT are excluded

• permissible spacer percent GC range set to [20, 80]

• spacers missing values for any score method (NA) are excluded

• (SpCas9 nuclease only) minimum permissible DeepHF and DeepSpCas9 scores set to 0.5

• spacers targeting repeat elements are excluded

• spacers overlapping SNPs are excluded

• (for GuideSets having gene annotation) spacers targeting the final 15% of the gene CDS (i.e., 3' end) are excluded

Filters will not be applied if the guideSet lacks the necessary annotation. For example, a guideSet lacking SNP annotation will not be filtered on the SNP criterium.

Value

A Shiny app object.

Examples

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

---

UI component for crisprShiny App

Description

UI component for crisprShiny App. Not intended for direct use.

Usage

crisprUI(id, cssFile = NULL)

Arguments

id	Module ID.
cssFile	Optional path of CSS file to be included in rendering app. NULL gives default styling, found in inst/www/styling.css.

Value

Shiny module UI component.

Examples

library(crisprShiny)
ui <- function(id){
    fluidPage(
        crisprUI(id)
    )
}

server <- function(id, gs){
    function(input, output, session){
        observeEvent(gs, {
            crisprServer(
                id,
                guideSet=gs,
                geneModel=NULL,
                useFilterPresets=TRUE
            )
        })
    }
}

myApp <- function(gs){
    shinyApp(ui=ui("id"), server=server("id", gs))
}

if (interactive()){
    data("guideSetExample_basic", package="crisprShiny")
    myApp(guideSetExample_basic)
}

---

Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS

Description

Example of a GuideSet object (with no additional annotation) storing gRNA sequences targeting the coding sequence of human gene KRAS (ENSG00000133703) for SpCas9 nuclease.

Usage

data(guideSetExample_basic, package="crisprShiny")

Format

A GuideSet object.

Details

The object was obtained by using crisprDesign::findSpacers on a GRanges of the CDS region of human gene KRAS. See code in inst/scripts/generateKrasData.R.

---

Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS

Description

Example of a fully annotated GuideSet object storing gRNA sequences targeting the coding sequence of human gene KRAS (ENSG00000133703) for SpCas9 nuclease.

Usage

data(guideSetExample_kras, package="crisprShiny")

Format

A GuideSet object.

Details

The object was obtained by applying all available add* annotation functions in crisprDesign on a GuideSet storing gRNAs targeting the CDS region of human gene KRAS. See code in inst/scripts/generateKrasData.R.

---

Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS

Description

Example of a GuideSet object storing gRNA sequences targeting the coding sequence of human gene KRAS (ENSG00000133703) for BE4max nuclease.

Usage

data(guideSetExample_kras_be, package="crisprShiny")

Format

A GuideSet object.

Details

The object was obtained by applying all base-editor-specific annotation functions in crisprDesign on the CDS region of human gene KRAS. See code in inst/scripts/generateKrasData.R.

---

Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS and NTCs

Description

Example of a fully annotated GuideSet object storing gRNA sequences targeting the coding sequence of human gene KRAS (ENSG00000133703) and some non-targeting controls (NTCs) for SpCas9 nuclease.

Usage

data(guideSetExample_kras, package="crisprShiny")

Format

A GuideSet object.

Details

The object was obtained by applying all available add* annotation functions in crisprDesign on a GuideSet storing gRNAs targeting the CDS region of human gene KRAS and some NTCs. See code in inst/scripts/generateKrasData.R.

---

List of tooltip annotations

Description

Tooltip messages for crisprShiny app stored in a list object.

Usage

data(tooltipAnnotation, package="crisprShiny")

Format

A list object.

Details

See code in inst/scripts/generateKrasData.R for tooltip annotations.

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Example of a GenomicRanges object storing annotated TSS ranges for the human gene KRAS

Description

Example of a GenomicRanges object storing annotated TSS ranges for the human gene KRAS (ENSG00000133703).

Usage

data(tss_kras, package="crisprShiny")

Format

A GenomicRanges object.

Details

The object was obtained by subsetting genomic ranges in tss_human from the crisprDesignData package for the KRAS gene (Ensembl ID: ENSG00000133703). See code in inst/scripts/generateKrasData.R.

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Example of a CompressedGenomicRangesList object storing annotated ranges for the human gene KRAS

Description

Example of a CompressedGenomicRangesList object storing annotated genomic ranges for the human gene KRAS (ENSG00000133703).

Usage

data(txdb_kras, package="crisprShiny")

Format

A CompressedGenomicRangesList object.

Details

The object was obtained by subsetting all genomic ranges annotations in txdb_human from the crisprDesignData package for the KRAS gene (Ensembl ID: ENSG00000133703). See code in inst/scripts/generateKrasData.R.

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