Getting started

This guide explains how to install and set up CellexalVR. Start by going to the download page to download CellexalVR. Before CellexalVR can be used, you must set up an HTC Vive and R. When you're done setting it up it could be a good idea to either read at least a little bit of the manual or if you don't like reading check out the videos at the video guides section.

1. The Hardware

CellexalVR requires a pretty powerful PC to work. We recommend you use a desktop machine with some specifications equivalent to an Intel i7 processor and an Nvidia GTX1080 graphics card. We also recommend you use an HTC Vive as your VR gear.
CellexalVR only runs on Windows 10.

2. Setting up the Vive


Click here for help on how to set up the HTC

The HTC Vive needs Steam VR to function with CellexalVR. If Vive setup program did not install this for you automatically for any reason, you can find it here. Run the SteamVR room setup (right click the Steam VR icon in the task bar and then click "Room setup") follow the on screen instructions.

3. Setting up the R package

CellexalVR assumes you have at least R 3.5.0 installed. If you do not, install it from here. Other versions of R should work but have not been tested properly.
Once R is installed you need to install the CellexalVR R package. Open up an R terminal as an administrator by right clicking executable (R.exe) and pressing "run as administrator". The R session needs to be run as an administrator in order for the package to be installed system wide, and not just locally.

If you do not have the devtools package installed you can install it by running the following command:

install.packages("devtools")

Once devtools is installed or if you already had it installed, you should run the following commands:

library(devtools)
install_github("sonejilab/cellexalvrr")

After some time the CellexalVR R package should be installed.

4. Installing Pandoc for creating HTML reports

Analysis made inside a CellexalVR session such as heatmaps, transcription factor networks and screenshots can be saved and compiled into a HTML report (read more here). To be able to do this the document converter Pandoc needs to be installed. Find the installation link here: Pandoc install.

5. Preparing your data

Your data needs to be processed by the CellexalVR R package before it can be loaded by CellexalVR. How to do just that is explained in our R tutorial.

If you want to try an already prepared dataset you can find some examples at the download page.

6. Installing CellexalVR

Drawing showing part of the folder structure.

For more information on how to download CellexalVR, see the download page. Once you have downloaded the zip archive, unpack it anywhere on you computer. You should see a folder called Data in the folder where the CellexalVR executable is, place your data exactly as the R package formatted it inside a new folder inside the Data folder. The image on the right shows you this folder structure.

7. Setting the R path

To access the R package we have installed we need to tell CellexalVR where it can find the R installation. When launching CellexalVR you will see a start menu. In this start menu there is a field to add the path to your R installation. You will only need to do this once unless you move the R installation to a new location or install a new version somewhere else.
Doing this will change a line in the config file from:
Or if you prefer, you can always open up the config.xml and change it there, find the line that says
<RscriptFilePath>REPLACE THIS TEXT WITH PATH TO R EXECUTABLE</RscriptFilePath>
and change it to the path to your RScript.exe, (note: not necessarily exactly like this):
<RscriptFilePath>C:\Program Files\R\R-3.5.0\bin\x64\Rscript.exe</RscriptFilePath>


Once you are finished setting up. Head on over to the manual to learn about the different possibilities. Or if you're feeling confident just launch CellexalVR and jump directly in and get started.