From dbb11256d351b987f1f56b7994f041a5e5ecf367 Mon Sep 17 00:00:00 2001 From: Stefano Beretta Date: Tue, 25 Feb 2025 16:08:34 +0000 Subject: [PATCH] Add new file --- MultiNicheNet/README.md | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 MultiNicheNet/README.md diff --git a/MultiNicheNet/README.md b/MultiNicheNet/README.md new file mode 100644 index 0000000..daf9b35 --- /dev/null +++ b/MultiNicheNet/README.md @@ -0,0 +1,5 @@ +#### Cell-cell interaction analysis #### +To explore the interactions of CAR-Ts with TAMs and DCs we employed **MultiNicheNet**, a method for differential cell-cell communication analysis among conditions. More precisely, this technique is designed to handle multi-sample, multi-group single-cell data by looking at cell-cell communication between the cell types in each sample and compare the resulting patterns between groups of interest.
+As a first step we extracted abundance and expression information from sender (CAR-Ts) and receiver (TAMs and DCs) cell types combining this expression of ligands in the senders to the corresponding receptors in the receivers. A set of affected target genes in the receiver was defined based on genome-wide differential expression analysis of receiver and sender cell types and subsequently used to predict the NicheNet ligand activities and NicheNet ligand-target links. NicheNet ligand-target links were finally used to prioritize all sender/ligand-receiver/receptor pairs and calculate their expression correlation with the predicted target genes. + +![IFN](./IFN.png)![P2A](./P2A.png)![Ortho](./Ortho.png) -- GitLab