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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Exporting Regulons #96

Closed rcw1 closed 5 years ago

rcw1 commented 5 years ago

Hi Bram,

I have a similar request, in my case the Regulons are the most important output from this pipeline, and I need to have them in a human readable format. I've looked for the JSON export command that you reference in this thread, but it's not clear what the command is. Can you write it here, or point me to where I can find it?

Thanks,

Rob

Dear Chris,

Just released a new version (0.8.7). This version includes your suggestion. Thanks.

Kindest regards, Bram

Originally posted by @bramvds in https://github.com/aertslab/pySCENIC/issues/16#issuecomment-404523318

bramvds commented 5 years ago

Dear,

This can be done via the Command Line Interface (CLI): the extension of the output file defines the format: GMT, CSV, JSON or YAML are available.

Hope this helps, Bram