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Shiny App to accompany CrispRVariants package
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README.md

Introduction

This github repository contains the code underlying the CrispRVariantsLite Shiny-based web app, which accompanies the main CrispRVariants package. This web app is primarily available from the Robinson lab web server at University of Zurich from the following link: CrispRVariantsLite. Instructions are given in the start up page of the app.

Example data

Example ZIP files (and corresponding TXT files with description of genome location and/or guide+PAM sequence) for the different entry points can be found in the /examples/ directory. If retrieving these files from the github repo, be sure to click on 'Raw' or 'View Raw'.

Running this app locally

The CrispRVariantsLite web app can be run locally, after installation of the necessary R packages (see below) and well as the command line tools: samtools, bwa mem and the indices for the organism of interest. After all this is completed, clone a version of this repository, set up the symbolic links (see the makelinks file) in the data/genome and data/txdb directories of the cloned repository and then the app can be run from the R console as:

#install.packages("shiny")  # only needed if 'shiny' package is not already installed
shiny::runApp( "/dir/to/CrispRVariantsLite/local/clone")

Installing all the R packages

The following packages will be needed by the web app:

source("https://bioconductor.org/biocLite.R")
library(BiocInstaller)
biocLite( c("CrispRVariants", "GenomicFeatures",
            "AnnotationDbi", "GenomicRanges",
            "IRanges", "Rsamtools", "Biostrings") )

install.packages("ggplot2",quiet=TRUE)
install.packages("shiny",quiet=TRUE)
install.packages("shinydashboard",quiet=TRUE)
install.packages("shinyBS",quiet=TRUE)
install.packages("rhandsontable",quiet=TRUE)

Other important details

The web application makes calls to bwa mem and samtools. Therefore, for every organism of interest, a bwa index will need to be created from the genome sequence. These need to be copied (or preferably, symbolically linked) to the data/genome directory; similarly, TxDb objects need to be saved to the data/txdb directory of the app. The convention used is that all the files ending in .fa in the data/genome are presented to the user in the dropdown menu of the web application. Importantly, the TxDB objects in the data/txdb directory must be named with the same prefix but a .sqlite extension. That is, if you are working with the hg19 genome, the application is expecting hg19.fa (and hg19.fa.XXX for all the bwa indices) in the data/genome directory and hg19.sqlite in the data/txdb directory.

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