Great demonstration! I have a question. You did not make use of any Chip-seq data although the authors used it in their application and mentioned it as a prior (the W matrix in the paper figure). How were you still able to get a posterior? how did the model know from the scRNA-seq data solely which genes are the TFs?
The priors are incorporated into their model automatically. No need for the user to input them. The model predicts TF activity regardless of the expression of TFs in the data. I.e., it looks at the expression of the TF targets. So it doesn't need to know which genes are TFs, but it does need to know targets which it can get from CHIP.
Dear sanbomic! I am wondering what is your first options for gene regulatory network analysis? when you have only single cell rna seq data or also have single cell ATAC data!!
Thank you for this video !
Great tutorial! Thanks!
Thank you! Glad you liked it!
Great demonstration! I have a question. You did not make use of any Chip-seq data although the authors used it in their application and mentioned it as a prior (the W matrix in the paper figure). How were you still able to get a posterior? how did the model know from the scRNA-seq data solely which genes are the TFs?
The priors are incorporated into their model automatically. No need for the user to input them. The model predicts TF activity regardless of the expression of TFs in the data. I.e., it looks at the expression of the TF targets. So it doesn't need to know which genes are TFs, but it does need to know targets which it can get from CHIP.
Dear sanbomic! I am wondering what is your first options for gene regulatory network analysis? when you have only single cell rna seq data or also have single cell ATAC data!!
I like scenic and scenic+ if you have paired ATAC data. Scenic and cell oracle are also good choices.
@@sanbomics Thank you so much
@@sanbomics Are you able to do a video on using scenic or pyscenic with scRNA seq data?