Example on running locally

[maximillo]

Hi Patrick,

I'm trying to get CellNet to work locally on my workstation, but I got error on step cn_salmon(stQuery) saying parrellel command not found. So I figured this step calls salmon using parallel. Then I installed parellel using conda but the problem persisted. On top of that, I'm not sure if I configured the paths properly. All parameter values default to what are supposed to be in the AMI. I wonder would you be able to provide a working example for local setup so I can understand it better. Thanks a lot!

Regards,
Max

[pcahan1]

We have now created a web application that takes as input an expression matrix (counts, TPM, or FPKM), and sample meta-data, and performs CellNet analysis. Additionally, this tool includes analysis of many state-of-the-art differentiation protocols, so that you can benchmark your results against those commonly used methds:

https://cahanlab.org/resources/agnosticCellNet_web/