There are many benefits to interface with Cytobank in the programming language R, including access to various helpful tools and automated workflows that provide extra functionality not easily done within Cytobank itself.
Before being able to utilize packages in R to interface with Cytobank such as the CytobankAPI and CytobankBridgeR package, there are several prerequisites that are required and are discussed in detail below. This guide will take you step by step through setting up a working R environment to start utilizing such packages.
1. A working version of R & RStudio
Download and install a working version of R from the official R website here and choose the correct operating system.
Recommended: Download RStudio, an integrated development environment (IDE) that makes it easy to use R once a working version of R is installed.
2. Install packages
Once a working version of R is installed, open up RStudio (or R) and install any packages that you may find useful via the following command:
Replace PACKAGE_NAME with any particular package you may find helpful. A few examples below show how to install the essential packages in order to interface with Cytobank.
3. Install essential Cytobank packages
Install the CytobankAPI package via the following console command:
(RStudio console window) (R console window)
Install the CytobankBridgeR package via the following console command: