6.0-Module6_Cell_Cell_Communication.Rmd

# Module 6: Cell Cell Communication  

 *<font color="#827e9c">By Gregory Schwartz, Veronique Voisin, Chaitra Sarathy and Ruth Isserlin</font>*
 
## Module 6 lecture : Cell-Cell Communication. 

Gregory Schwartz

[Lecture](./lectures/Pathways_2024_module6_Schwartz.pdf)

  
## scRNA lab praticals

[scRNA-lab1_PBMC](#scRNA_PBMC)

 - 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.

[scRNAlab2_Glioblastoma](#scRNA_glioblastoma)

 - Similar to lab1, we extracted gene lists from scRNA clustering from glioblastoma data.

 - We created a mastermap by uploading in EnrichmentMap the pathway enrichment results for all the cluster gene lists.
 
[scRNAlab_CellPhoneDB](#scRNA_cellPhoneDB)

 - Similar to lab1 , we start from scRNA data from peripheral blood mononuclear cells and we are going to study the cell-cell communication between different cell types using CellPhoneDB. 

 
[scRNAlab_NEST](#scRNA_NEST)

 - In this lab, we are exploring cell-cell communication in spatial trancriptomic of a pancreatic cancer (PDAC) tissue section using the tool NEST.