Chapter 1 Prerequisites

Congratulations on your CODEX experiment! In this CODEX data analysis guide we provide instructions for CODEX data analysis to enable discovery via spatial biology.

1.1 Requirements

R>4.0, RStudio, rtools40, Anaconda, Fiji, CODEX MAV

1.1.1 Installation of R, Rstudio, and Rtools.

1.1.1.1 Install R

Download and install the most recent version of R from Cloud_r-project.  Important Note If you currently use Akoya Biosciences’ inForm Tissue Analysis products, please do not uninstall version 3.1.0. If you accidentally uninstall version 3.1.0, please re-install.

1.1.1.1.0.0.1 Install Working Development Environment

Install one of the following: – Windows Users: Install Rtools – Mac Users: Install Xcode

1.1.1.2 Install Rstudio

Download and install the desktop version of Rstudio

1.1.1.3 Install Fiji and CODEX MAV

Follow directions provided at help.codex.bio

1.1.1.4 Install Anaconda