We have protocols for using SPADE (matlab), tSNE/viSNE (FlowJo 10.2, matlab/Cyt). We are also in the process of uploading protocols for PhenogGraph (R) and FlowSOM (R), among other tools. For non-registered users, you can request access to these protocols at this link. For registered users, click here:
Additionally, a number of helpful scripts can be found at: www.github.com/sydneycytometry.