I am trying to find a toll/ software/ package that can identify cell specific pathways in ScRNA-seq data. I have analyzed the data and has expression matrix per cell type. I googled only two studies – https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582408/ another issuing RF https://ieeexplore.ieee.org/document/8854213 Since now the technology is very well developed, any on eon the forum is working on this topic may have experience in identifying cell specific networks. Any feedback or pointer to a robust or good toll will be highly appreciated.
You can use standard enrichment tools (clusterProfiler, enrichR, g:profiler, etc) for cluster markers - they'll work just fine since they just take gene lists. If you want to do single sample GSEA on each cell, I'm going to plug a new R package called escape that I've been working on with a collaborator. It's quite easy to use and works with a counts matrix, Seurat object, or SingleCellExperiment object. It should be included in the next Bioconductor release.