**Expression analyses**

This folder contains scripts used to perform transcriptomic analyses including differential expression analyses (DESeq2 and EVE), co-expression analyses, deconvolution and visualization.

0-count_table_prep_all_cds.Rmd --> prepare the count table after ropipe pipeline

1-Expression_master.Rmd --> launch differential expression analyses with DEseq2. It calls functions from script 1-Expression_master_lib and supplementary files stored in extra_files_for_DE folder

1-Expression_master_lib.R --> Contains functions to perform DE analyses, as well as dendrograms based on expression.

2-Expression_simulation_master.Rmd  --> launch permutation test on the differential expression analyses. It calls functions from script 2-Expression_master_lib_simu.R. 

2-Expression_master_lib_simu.R

3-EVE_inference_simulation.R --> Run differential expression analyses with EVEmodels.

4-WGCNA_master_June2025.Rmd --> launch co-expression analyses. It calls functions from script 4-WGCNA_master_lib_June2025.R

4-WGCNA_master_lib_June2025.R --> Compute WGCNA module construction and trait correlation

4-WGCNA_Heatmap.R --> heatmap visualization from WGCNA results

5-Enrichment_clusterProfiler.R --> Compute GO enrichment using clusterProfiler package

5-EnrichResult_in_network.Rmd --> Draw network-like plot from enrichment results

6-Deconvolution_rat_scRNAseq_final.qmd --> Script to perform deconvolution analyses using rat as scRNA-seq reference dataset

7-Pairwise_analysis.qmd --> script to compute analyses represented in Figure 6.