VisProDom: an interactive Shiny/R application to display protein domains with transcriptional features

GNU General Public License, GPLv3

Installation

install compiler

The install_github(), in the R package remotes, requires that you build from source, thus make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

• For Windows system, rtools, a compiler, is required and can be found at https://cran.r-project.org/bin/windows/Rtools/.

• For Ubuntu/Linux system, compilers could be installed by the command: sudo apt-get install libcurl4-openssl-dev libssl-dev. For more information, please see https://stackoverflow.com/questions/20923209/problems-installing-the-devtools-package.

• install R package devtools and remotes

install.packages(c("devtools","remotes"))

install depended packages, including ggplot2, shinydashboard, shiny, ggplot2, rintrojs, dplyr, data.table, ggrepel

#ggplot2, ggrepel, and reshape2 are installed from CRAN
install.packages(c("ggplot2", "shinydashboard", "shiny", "ggplot2", "rintrojs", "dplyr", "data.table", "ggrepel","markdown"))

install VisProDom from GitHub:

library(remotes) # version 2.1.0
#download, build, and install VisProDom without creating vignette
install_github("whweve/VisProDom")
#download, build, and install VisProDom with creating vignette
install_github("whweve/VisProDom",build=TRUE,build_vignettes = TRUE)

example

#load VisProDom
library(VisProDom)
# initiate VisProDom shiny appp
runVPDapp()