Spatial Visium 10x script for analysis with Bacterial Probes

Script and tools used for the study:

Dual Spatial Host-Bacterial Gene Expression in Mycobacterium abscessus Respiratory Infections

Di Marco and Nicola et al., Communications Biology 2024

Data available at: GSE242471

Spatial data analysis using Seurat

• Integration.R:
  Script for importing data from spaceranger output and perform deconvolution and integration

• ClusterAnalysis.R:
  Script for Cluster analysis, markers detection

• InfectedTissueAnalysis.R:
  Script for analysis of Infected tissues, markers detection, MABS+ vs MABS- analyses, and probes UMI counts

• Markers.R:
  Script for analysis of INOS, ROS, Hypoxia markers and probe location