Update README.md

README.md

@@ -4,7 +4,7 @@
 
 Notaro M, Monti M, Beretta S, Merelli I, Squadrito M, _et al._; 2025
 
-Corresponding Author: Mario Leonardo Squadrito. Email: squadrito.mario@hsr.it
+Corresponding Author: Mario Leonardo Squadrito. Email: squadrito.mario@hsr.it.  [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40Mariosqua)](https://x.com/Mariosqua)
 
 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)
@@ -15,31 +15,27 @@ ENA: [PRJEB78386](https://www.ebi.ac.uk/ena/browser/view/PRJEB78386)
 - 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
+        - 001_TAD012_APCs_analysis_liver.R
+        - 002_TAD012_Liver_Tetramer_and_CD4_GSEA_DOTPLOT.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
+        - 001_TAD018_liver_tumor_APCs_MLS_dotplotstellari_radarplot.R
+        - 002_TAD018_Liver_Tumor_TNK_dotplot_radar_GSEA.R
+        - 003_TAD018_Alluvial_plot.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
+        - 001_TAD019_APCs_analysis.R
+        - 002_TAD019_TandNK_analysis.R
+        - 003_TAD019_Multinichnet_Tumor.R
     - Vizgen
-        - heatmap_transcript_distance_simplified.R
+        - Vizgen_transcript_distance_heatmap.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
+    - miDB_sig4.MLS.rds: 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).