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cailab-tamu / scTenifoldKnk

R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
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Questions about running scTenifoldKnk #16

Closed abedkurdi closed 2 years ago

abedkurdi commented 2 years ago

Hello there, I would like to ask a few questions about scTenifoldKnk: is it mandatory to run the tool on an entire sample? Is it possible to run it on a specific cluster in a single-cell sample after clustering and annotation? What do you recommend to use: normalized or not normalized counts?

Thank you in advance.

dosorio commented 2 years ago

Hi @abedkurdi,

Thanks for using scTenifoldKnk. The input depends on the question you may want to solve. For example, if you are interested in knowing the function of a gene in a tissue, you can use the entire dataset, but if you are interested in cell-type specific roles, you may use a single cluster instead.

If you normalize the data before input, please use a normalization that produces only positive values and deactivate the quality control step with QC=FALSE

Please let me know if you have any other questions,

Best wishes,

Daniel

abedkurdi commented 2 years ago

Thanks a lot!