ColocalizR is an R-based image-analysis application developed for the quantification of co-localization in high-throughput, on a cell-by-cell basis.
ColocalizR can be used on Windows, Linux and MacOS X, with at least 8GB of RAM and a quad-core (or higher) last-generation CPU. Internet connection is required for installation.
Click on the previous links to download and install all the required program files.
Install the program files in the same way than in Windows configuration. On Mac, Java is not required but you have to install Xcode either by downloading it via the AppStore or by installing it directly via the terminal. The easiest way on MacOS 10.9 or later is to type in a terminal:
It will be asked you to install Command Line Tools, you just have to click on Install in the pop-up window.
For previous versions of MacOS, you can refer to these instructions to install basic programmation tools on Mac (including Xcode).
On Linux, you can either install the program files in the same way than in the two previous configurations or use command lines to do it. If you choose to do it in command lines, type in a terminal the commands below to correctly install and configure R, RStudio and Java.
grep -q -F "deb http://cran.rstudio.com/bin/linux/ubuntu *UbuntuVersion*-cran35/" /etc/apt/sources.list || sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu *UbuntuVersion*-cran35/" >> /etc/apt/sources.list sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 sudo apt update sudo apt install r-base
grep -q -F "deb http://cran.rstudio.com/bin/linux/debian *DebianVersion*-cran35/" /etc/apt/sources.list || sudo su -c "echo 'deb http://cran.rstudio.com/bin/linux/debian *DebianVersion*-cran35/' >> /etc/apt/sources.list" sudo apt install dirmngr sudo apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF' sudo apt update sudo apt install r-base
wget https://download1.rstudio.org/rstudio-1.1.456-amd64.deb sudo dpkg -i rstudio-1.1.456-amd64.deb sudo apt install -f # install missing dependencies
sudo apt install -y default-jre sudo apt install -y default-jdk sudo R CMD javareconf
sudo apt install libcurl4-openssl-dev libssl-dev unixodbc unixodbc-dev libtiff-dev fftw-dev fftw3 fftw3-dev
You have then to install some packages before running the application. To do so, open RStudio and copy/paste the lines below in the console :
install.packages(pkgs=c('rJava','devtools','R6','shiny','tiff','reshape','reshape2','RODBC','foreach', 'doParallel','stringi','rChoiceDialogs','gtools'), repos = "http://cloud.r-project.org") source("http://bioconductor.org/biocLite.R") biocLite(pkgs=c('EBImage','flowCore'), ask=F) devtools::install_github(c("kroemerlab/MetaxpR","kroemerlab/MorphR","kroemerlab/ColocalizR"))
Once all is installed, you can run this line in the console to download and launch the app.
For more informations, please refer to the User Manual.