In mrkbrtkhn/cTagPipe:

knitr::opts_chunk$set(echo = TRUE)

About cTagPipe

This application aims at the identification of DNA sequences that allow the C-terminal tagging of endogenous loci in order to express fusion proteins. To achieve this, a combination of CRISPR/Cas9-mediated induction of DNA breaks and homologous recombination mediated repair with engineered repair templates is applied.

The application mainly works as a Shiny app but can be run from the R command line, too. The user selects the gene of interest and the pipeline calculates CRISPR guide RNAs, selects recombination templates and modifies/mutates the templates if required as such, that the guide RNAs will not be able to allow cutting of the recombined locus.

Installation

Please install the latest version of R from https://www.r-project.org. On Ubuntu you will have to install a number of system packages in order to make the subsequent installation of R packages possible.

```{sh message=FALSE, warning=FALSE, comment=FALSE,results='hide',eval=FALSE} sudo apt-get install libssl-dev sudo apt-get install libcurl4-openssl-dev sudo apt-get install libxml2-dev

In order to install this package, R's devtools package is required:

```r
listOfPackages <- c("devtools")
newPackages <- listOfPackages[!(listOfPackages %in% installed.packages()[,"Package"])]
if (length(newPackages)>0) {
  source("https://bioconductor.org/biocLite.R")
BiocInstaller::biocLite(newPackages)
}

This enables you to install directly from GitHub repository:

library(devtools)
install_github("mrkbrtkhn/cTagPipe")

Most likely this will produce a lot of errors. Dependencies are still a mess and I currently have no time to work on them. Please install them manually.

Running cTagPipe functionality:

Assuming you have managed to install cTagPipe, the following code will start a Shiny server with the functionality as it is yet implemented:

library(cTagPipeTest)

distanceBetweenGuides <- 100
recArmLength<-150
removeAddGeneHits <- TRUE
browserWindow<-200

### target sequences
seqs<-readDNAStringSet(system.file('extdata','rec_sequences.fa',package='cTagPipeTest'))

mAID <- seqs$mAID
tripleFlag<- seqs$triple_FLAG
t2A<- seqs$t2A
fiveP<- seqs$`5_prime_PITCH`
threeP<- seqs$`3_prime_PITCH`
neoM<- seqs$NeomycinR
hygM<- seqs$HygromycinR


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## Only run examples in interactive R sessions
if (interactive()) {

  ui <- shiny::fluidPage(
    shiny::pageWithSidebar(
      shiny::headerPanel('C-terminal tagging pipeline'),
      shiny::sidebarPanel(
        shiny::selectInput('myGene', 'Transcript ID', c("NM_001304504","NM_153252","NM_001273",
                                                        "NM_000237","NM_002106","NM_138635","NM_014660",
                                                        "NM_175061","NM_030665","NM_005650","NM_001141969",
                                                        "NM_003325","NM_003496","NM_014034","NM_020713",
                                                        "NM_001203258","NM_004689","NM_006565","NM_080618",
                                                        "NM_002875","NM_133487","NM_003883","NM_021975",
                                                        "NM_001077700","NM_052927","NM_012308","NM_000937",
                                                        "NM_001004456","NM_001278215",
                                                        "NM_001077700")),
        shiny::selectInput('myGenome', 'Genome', c("hg38")),
        shiny::numericInput('winSize', 'Window Size', 100, min = 50, max = 150),
        shiny::selectInput('myCassette', 'Rec. template', c("PITCH/homolgy_arm/AID/tripleFLAG/T2A/homolgy_arm/PITCH")),
        shiny::actionButton('run', 'Run'),
        width = 3
      ),

      shiny::mainPanel(#width=800,
        shiny::tabsetPanel(
          shiny::tabPanel("Analysis report",shiny::verbatimTextOutput("testout")),
          shiny::tabPanel("Plot", shiny::plotOutput("plot1")),
          shiny::tabPanel("CCTop summary", DT::dataTableOutput("ccSumTable", width = 800)),
          shiny::tabPanel("CCTop results", DT::dataTableOutput("ccbindTable", width = 800)),
          shiny::tabPanel("Guide pairs", DT::dataTableOutput("pairwiseSelections", width = 800)),
          shiny::tabPanel("Alignment test", msaR::msaROutput("msa", width="100%")),
          shiny::tabPanel("Sequences", shiny::verbatimTextOutput("seqSummary")),
          shiny::tabPanel("Mutation view guide 1", DT::dataTableOutput("mutView1", width = 1000)),
          shiny::tabPanel("Mutation view guide 2", DT::dataTableOutput("mutView2", width = 1000))
        )
      )))

  shiny::shinyApp(ui, server)
}