README.md

# Squadrito_LiverTumor2022_Spatial

Kerzel T, Giacca G, Beretta S, et al.
**In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases.**
2022.


GEO: [GSE221359](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221359)

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### Directories and Files ###
- SampleSheet.csv: names of samples and corresponding treatment condisions
- scripts: folder with R scripts used for the analyses
  - `0_Compute_Zones.R`: initial analysis with Full object creation and zonation;
  - `1_GSEA_Visualization.R`: analysis on zones with GSEA;
  - `2_SigZones_Visualization.R`: in depth characterization of zones with signatures.
- data: results of the analyses
  - GSEA_Zones_unique_integrated.res01.txt: GSEA results;
  - Zones_unique.integrated.txt: results of zonation;
  - crc.integrated_metadata.csv.gz: metadata of the final object;
  - miDB_sig3.rds: signatures for GSEA from MSigDB.

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### Analyses ###

Spatial Transcriptomics data of Liver Tumor paper.