RNA-seq count data as input
Hi Gaia Zaffaroni,
This method is very interesting and especially the integration of signalling pathways to prioritize signalling molecules.
I would like to identify signalling molecules for differentiation from one cell type to another and I have RNA-seq gene expression count data for the 2 cell states. However, I noticed that the input gene expression data for this pipeline are in microarray format (*.CEL files). Please let me know whether this pipeline accepts RNA-seq count data and the best way to implement this method for RNA-seq gene expression data.
Another question regarding the integration of signalling pathways from MetaCore. To obtain the MPP, are all the human signalling pathways available in MetaCore queried OR is the search constrained to a subset of signalling pathways used in this paper.
Thanks and Regards,
Uma