This repository contains the code used to analyize Flu Spatial Sequencing data.
We utilize Visium and Spotlight to determine spatial associations between the immune system inflamation and lung tissue fibrosis. Additionally, we investigate how these cells and sptial associations are changed between young and aged conditions.
Single-cell datasets of lungs for young and old datasets were also sequenced and analyized. This was done through seurat to determine different cell types and differential gene expression. Furthermore, cellchat was used to determine cell to cell interactions.
The results of this study can be found in our paper: A spatial sequencing atlas of age-induced changes in the lung during influenza infection.