This page is probably only relevant to you if you have some programming knowledge.
CellexalVR is an open source program and can be customized in a number of ways. You can check out the source code here and the offical documentation here. The CellexalVR front end is written mostly in C# using the Unity3D engine. An introduction to the ideas and code behind CellexalVR can be found here.

The back end that does all the statistical analysis is written in R. The back end is also open source and you can check out the source code here. If you wish to use a different way to choose which genes are displayed on a heatmap, or which genes are in a network, the R scripts that produce the files that define those are located in the CellexalVR_Data/StreamingAssets/R folder. These R scripts don't contain much code themselves, but rather just calls functions defined in the CellexalVR R package. Feel free to modify these, but make a back up first.