In my PhD thesis, I developed a method and software package to infer interactions and cell states from gene expression data. Both the software and the research are now published!
The software is called Stator, and comprises the Stator Nextflow pipeline, as well as a bespoke Shiny app developed by Yuelin Yao.
We used it to find previously hidden differentiation states in the embryonic mouse brain and sub-phases of the cell cycle, and discovered liver tumour cell states that are prognostic of patient survival. Please get in touch if you are interested in using Stator for your own research!