Update README.md

README.md

 # Notaro_Mouse_LM_2025
 
+**_In vivo_ armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation**
+
+Notaro M, Monti M, Beretta S, Merelli I, Squadrito M, _et al._; 2025
+
+Corresponding Author: Mario Leonardo Squadrito. Email: squadrito.mario@hsr.it
+
+GEO: [GSE273615](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE273615)
+ENA: [PRJEB78386](https://www.ebi.ac.uk/ena/browser/view/PRJEB78386)
+
+
+## Directories and Files
+
+- environment_singlecell5.yml: contains the conda virtual environment that can be used to install all the dependencies.
+- scripts: folder with R scripts used for the analyses
+    - TAD012
+        - 001_APCs.analysis_liver_12_FINAL_MM.R
+        - 002_Liver_Tetramer_and_CD4_GSEA_DOTPLOT_12_Final_MM.R
+    - TAD018
+        - 001_liver_tumor_APCs_MLS_dotplotstellari_radarplot_FINAL_MM.R
+        - 002_Liver_Tumor_TNK_dotplot_radar_GSEA_FINAL_MM.R
+        - 003_Alluvial.plot_FINAL_MM.R
+    - TAD019
+        - 000_subsetting.R
+        - 001_APCs.merged_analysis_19_FINAL_MM.R
+        - 002_TandNK.merged_analysis_19_FINAL_MM.R
+        - 003_Multinichnet_Tumor_TAD19_MM.R
+    - Vizgen
+        - heatmap_transcript_distance_simplified.R
+        - Vizgen_transcript_distance.R
+    - Others
+        - plot_stellare_function.R
+        - seurat_init.R: seurat analysis pipeline part 1;
+        - seurat_final.R: seurat analysis pipeline part 2;
+        - useful_functions.R: contains functions for UMAP, featureplots, Violin plots;
+- data: results of the analyses
+    - plots
+    - tables
+- reference
+    - regev_lab_cell_cycle_mouse.rds: contains the genes involved in the cell cycle in mouse
+    - GSEA: reference files for GSEA analysis
+
+## scRNAseq analysis
+The initial preprocessing of the data, including mapping against the _Mus musculus_ GRCm38 reference genome and gene counting, was done using the 10x Genomics Cell Ranger Software (v7.2.0) using default parameters. The resulting data were imported into R and analyzed with the Seurat package (v5.0.1).
+