MoPAC Files

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INSTALLATION
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MoPAC is an R package which may be installed through the following command in a terminal running R or in the Rstudio console:

install.packages("MoPAC_0.3.1.tar.gz",repos=NULL,type="source")

It might take over a minute to install due to the large size of the STRING gene interaction dataset.

Dependencies:
Several R packages must be installed beforehand for the installation to be successfull:

install.packages("Rcpp")
install.packages("gtools")
install.packages("stringr")
install.packages("openxlsx")
install.packages("tensorA")
install.packages("ineq")
install.packages("reshape2")
install.packages("plyr")
install.packages("ggplot2")
install.packages("gplots")
install.packages("ggrepel")
install.packages("gridExtra")
install.packages("knitr")
install.packages("rmarkdown")
install.packages("shiny")
install.packages("shinyBS")
install.packages("shinythemes")
install.packages("shinyFiles")
install.packages("DT")
install.packages("visNetwork")
install.packages("sqldf")
install.packages("rhandsontable")
install.packages("neat")
install.packages("igraph")

Optional dependencies:
The "STRINGdb" R package is optional but highly recommended for enhanced visualization of gene interaction networks:

source("https://bioconductor.org/biocLite.R")
biocLite("STRINGdb")

If you wish to generate pdf and html reports, which is an optional feature, additional distribution-specific installations are necessary, for example in Fedora/RedHat/CentOS:

sudo yum install libpng-devel
sudo yum install openssl-devel
sudo yum install libcurl-devel
sudo yum install pandoc
install.packages("plotly")

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USAGE
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Once installed, the interactive user interface may be started through the following two commands in a terminal running R or in the Rstudio console:

library(MoPAC)
run.MoPAC()

Instructions are provided within the interface. A video tutorial to reproduce the results in our publication is provided in the following link: https://www.youtube.com/watch?v=D2Wd-ON69QQ

The results were published at:
Gao, G. et al. PRMT1 loss sensitizes cells to PRMT5 inhibition. Nucleic Acids Res. (2019). doi:10.1093/nar/gkz200

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VERSION HISTORY
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0.3.1
Added a sample sgRNA library file to be used in the upcoming tutorial.

0.3.0
Source code using the new methodology.

0.2.0
Improved interface and bug fixes for the method used in the Gao et al. publication.

0.1.0
Source code of the method originally used in the Gao et al. publication.