Before you start; you will have to install R and/or RStudio. You can install DEBrowser from bioconductor or from the source code. Install the required dependencies by running the following commands in R or RStudio. Please check Operating System Dependencies section, in case your operating system requires packages to be installed.
A.1 Bioconductor Installation (Recommended):
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("debrowser")
A.2 Bioconductor Installation - Developer Version:
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("debrowser", version = "devel")
B. Installation instructions from source code:
install.packages("devtools") ## If you haven't installed devtools, you can easily install it by using this command library("devtools") install_github("UMMS-Biocore/debrowser", build_vignettes = TRUE)
Alternatively, you can download the source code from here as a compressed format. Then you need to decompress and install with following command:
R CMD INSTALL debrowser-develop ##where folder name is debrowser-develop
After debrowser installation, you can load and start DEBrowser by following commands:
Once you run
startDEBrowser() shiny will launch a web browser which is ready to use!
For more information about DEBrowser, please visit our Quick-start Guide section within documentation.
Operating System Dependencies¶
On Fedora/Red Hat/CentOS, these packages have to be installed:
openssl-devel, libxml2-devel, libcurl-devel, libpng-devel
On Ubuntu 18.04 LTS, you can install required packages by following command:
sudo apt-get install libcurl4-openssl-dev libssl-dev libv8-3.14-dev udunits-bin libudunits2-* libxml2-dev