Moni - Multiomics data integration unveils core transcriptional regulatory networks governing cell type identity
Reconstruct mechanistic core gene regulatory networks from RNA-seq, epigenetic, protein-protein interaction and TF ChIP-seq datasets.
- bedtools v2.24.2.1 (https://bedtools.readthedocs.io/en/latest/)
- R v4.0 or greater
This R-package provides the basic functionality for network reconstruction. The main functions to be used are preprocess_ArchS4, computeJSDSingle, generateNetwork, generateNetworkLogic. If a background gene expression dataset has to be generated, the user first has to download R-scripts from ArchS4 that download the desired files and subsequently call preprocess_ArchS4 with the directory of the downloaded R-scripts as a parameter. Afterwards, the background can be used to compute the Jennsen-Shannon-Divergence of a query sample with respect to the background for selecting core TFs. Given epigenetic data and a list of core TFs and expressed TFs, generateNetwork can then be used to obtaine the interactions between the core and neighboring TFs. Finally, generateNetworkLogic will create the logic rules. More documentation about the parameters can be found in the help-files of each function.