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Original scripts for the manuscript "Sex shapes cell-type-specific transcriptional signatures of stress exposure in the mouse hypothalamus", Brivio et al. Cell Reports, 2023

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

Brivio et al., 2023 Cell Reports

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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)

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Original scripts for the manuscript "Sex shapes cell-type-specific transcriptional signatures of stress exposure in the mouse hypothalamus", Brivio et al. Cell Reports, 2023

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