README.md

Sex shapes cell-type-specific transcriptional signatures of stress exposure in the mouse hypothalamus

Brivio et al., 2023 Cell Reports

This repository contains the scripts for the original analysis from the manuscript.

Web App

This dataset is freely explorable at the following link.

Content structure

Sex x Stress repository  
├── README.md 
└── code
    ├── scRNA-seq analyses (R scripts)  
    │    ├── Whole dataset   
    │    │   ├── Ambient_RNA.R                      # Ambient RNA calculation  
    │    │   ├── Function_stability_reclustering.R  # function to calculate stability in neurons reclustering
    │    │   ├── Neurons_reclustering.R             # Neurons reclustering  
    │    │   └── Distance_backgrounds.R             # Distance of ARS response between backgrounds   
    │    └── Oligodendrocytes analysis  
    │         ├── OL_DEGs_clustering.Rmd            # Genes clustering  
    │         ├── OL_pseudotime.R                   # Pseudotime analysis 
    │         └── OL_CCInx.R                        # CCInx permutation analysis 
    │  
    └── RNAscope analysis (python and groovy scripts)  
        ├── RNAscope_processing_part1_images_preparation.groovy         # Images preparation (groovy)  
        ├── RNAscope_processing_part2_images_preprocessing.ipynb        # Images preprocessing (py)
        ├── RNAscope_processing_part3_roi_expansion_nooverlap.groovy    # ROI espansion (groovy)  
        └── RNAscope_processing_part4_signal_identification.ipynb       # Signal detection (py)