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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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using scenic on bulk expression data? #60

Closed yuliusema4 closed 5 years ago

yuliusema4 commented 5 years ago

Hi

Can we do that? my feeling is we can, only the interpretation is different.

Best

Yu

bramvds commented 5 years ago

Hi Yu,

This could indeed be done. For your reference, SCENIC evolved from the following paper which applied GENIE3 to a multi-condition bulk RNAseq data set followed by pruning of indirect target using the previously published cisTarget method:

Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. Delphine Potier, Kristofer Davie, Gert Hulselmans, Marina Naval Sanchez, Lotte Haagen, Vân Anh Huynh-Thu, Duygu Koldere, Arzu Celik, Pierre Geurts, Valerie Christiaens, Stein Aerts Cell Reports 2014 https://dx.doi.org/10.1016/j.celrep.2014.11.038

Hope this helps, Bram