Cell type pathway ScRNAseq

Question

[kanwarjag]

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.

[jrleary]

Along the other suggestions, I'll add the VAM package implemented in this preprint: Variance-adjusted Mahalanobis: a fast and accurate method for cell-specific gene scoring. I don't think the package is up on GitHub / CRAN yet, but if you contact the author he's happy to share the compiled .tar.gz package file. It works really well in my experience. It takes Seurat objects as input along with a list of gene sets to test, and computation time isn't long. I've been using it in my analyses for a couple months now.

[kanwarjag]

Any comments/ feedback please?

[rob.costa1234]

I am also interested to know what pathway tool is used for single cell RNA seq data.

[ATpoint]

What is wrong withthe suggestions from 2 years ago? pathway for single cell RNA-seq

Answer 1

[jared.andrews07]

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.