Module 6: Review of the tools
By Veronique Voisin, Chaitra Sarathy and Ruth Isserlin
scRNA lab praticals
This lab starts from scRNA data from peripheral blood mononuclear cells.
The cells from similar cell types were grouped into clusters.
We extracted the gene lists corresponding to each cluster and run pathway analysis on it using g:Profiler.
We also created pseudobulk from the data, ran GSEA and created an enrichment map.
Similar to lab1, we extracted gene lists from scRNA clustering from glioblastoma data.
We created an mastermap by uploading in EnrichmentMap the pathway enrichment results for all the cluster gene lists.
- scNetViz is a Cytoscape that download scRNA data from the SingleCellAtlas, calculated differential expression between clusters or defined catergories and create protein-protein interaction networks out of it.
Integrated assignment
- In this integrated assignment, all the tools viewed during the workshop from module 1 to module 5 are integrated. The dataset is a microarray dataset available publicly from GEO.