ColocalizR

ColocalizR is an R-based image-analysis application developed for the quantification of co-localization in high-throughput, on a cell-by-cell basis.

Requirements

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.

Installation

To use this app, you need to have R, RStudio, Java and Strawberry Perl installed.

Windows

Click on the previous links to download and install all the required program files.

MacOS X

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:

xcode-select --install

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).

Linux (Ubuntu/Debian)

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.

Install dependencies

sudo apt install libcurl4-openssl-dev libssl-dev unixodbc unixodbc-dev libtiff-dev fftw-dev fftw3 fftw3-dev libv8-3.14-dev libv8-3.14-dev perl

Install R

Ubuntu

grep -q -F "deb http://cran.rstudio.com/bin/linux/ubuntu *UbuntuVersion*-cran*Rversion*/" /etc/apt/sources.list || sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu *UbuntuVersion*-cran*Rversion*/" >> /etc/apt/sources.list
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt update
sudo apt install r-base

Debian

grep -q -F "deb http://cran.rstudio.com/bin/linux/debian *DebianVersion*-cran*Rversion*/" /etc/apt/sources.list || sudo su -c "echo 'deb http://cran.rstudio.com/bin/linux/debian *DebianVersion*-cran*Rversion*/' >> /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

Install RStudio

wget https://download1.rstudio.org/rstudio-*RStudioVersion*-amd64.deb
sudo dpkg -i rstudio-1.1.456-amd64.deb
sudo apt install -f  # install missing dependencies

Install Java

sudo apt install -y default-jdk
sudo R CMD javareconf

R Packages

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'), repos = "http://cloud.r-project.org")

# For R versions < 3.5
source("http://bioconductor.org/biocLite.R")
biocLite(pkgs=c('EBImage','flowCore','S4Vectors'), ask=F)

# For R versions >= 3.5
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("EBImage","flowCore","S4Vectors"), version = "3.8")

devtools::install_github(c("kroemerlab/MetaxpR", "kroemerlab/MorphR", "kroemerlab/ColocalizR"))

⚠️ ColocalizR requires version 4.20.1 (or later) of EBImage ⚠️

Application

Once installation is complete, you can run this line in the console to launch the app. library(ColocalizR);Launcher()

For more informations, please refer to the User Manual.