Installation Instructions

Versions

Both the latest stable releases of all Cytoverse packages and more up-to-date development builds can be installed from Bioconductor. If you have not already done so, you will need to install BiocManager by running the following in R:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

The most up-to-date development versions can also be built from sources available from Github. If you are building from source on Windows, you will need to install Rtools and will need to follow some additional instructions for installing RProtoBufLib.

Bundled Installation

The easiest way to install the cytoverse packages is by using the cytoverse installer package. It will show you all of the packages that will be installed before proceeding. This package can be used to later update cytoverse packages from either Bioconductor or GitHub.

To install from the stable Bioconductor releases:

remotes::install_github("RGLab/cytoverse")
cytoverse::cytoverse_update()

To install from the development branches from GitHub:

remotes::install_github("RGLab/cytoverse")
cytoverse::cytoverse_update(repo = "github")

Individual Packages

Installing or updating additional RGLab packages can be done in a similar manner, either by utilizing the cytoverse installer package:

cytoverse::cytoverse_update(pkgs = "flowStats")

or manually from Bioconductor:

BiocManager::install("flowStats")

or manually from GitHub:

devtools::install_github("RGLab/flowStats")

Cytoverse -> FlowJo

The entire Cytoverse collection of packages is open-source and available from the repositiories listed above, with the sole exception of the functionality to convert Cytoverse GatingSet objects in to FlowJo workspaces. This functionality is provided in the form of a Docker image so it will work on any user operating system so long as Docker is installed.

This is not required for using any other parts of the Cytoverse, but if it is functionality you require, please follow Docker’s installation instructions and then follow these instructions to get the appropriate docker image from Docker Hub:

  • If you have installed the packages from a particular Bioconductor release:
    1. Determine the major and minor version of your cytolib installation by using the following command in R:
    packageVersion("cytolib")
    
    1. Pull the docker image tagged with the corresponding major and minor cytolib version. For example, if the command above returns that your cytolib version is 2.0.2, you should use:
    docker pull rglab/gs-to-flowjo:2.0
    
  • If you have installed the packages from the current GitHub development branches, please pull the “devel” tagged image. For example:
    docker pull rglab/gs-to-flowjo:devel
    

While you can use this tool directly from the command line following the usage instructions here, you can also simply use the gatingset_to_flowjo method from the CytoML package after you have obtained the Docker image using the above docker pull command.

Cytoverse Docker Image

Docker images are also provided based on the Docker images available from Bioconductor, with the Cytoverse packages pre-installed. These Cytoverse Docker images are also available from the RGLab Docker Hub page.