eviho/10XHip2021_VihoEMG

Cell type specificity of glucocorticoid signaling in the adult mouse hippocampus

Viho EMG et al. 2021 - Journal of Neuroendocrinology

DOI: https://doi.org/10.1111/jne.13072

Project description

This repository contains the details of the algorithms the authors used for single-cell analysis, coupling heatmaps and gene regulatory analysis.

1. Pre-processing according to Seurat standard workflow (R v3.6.1)
2. Gene expression: pre-processing and visualization of the gene expression matrix (R v3.6.1)
3. Co-expression: generation of coupling heatmaps (R v3.6.1)
4. pySCENIC: scalable Python SCENIC workflow (Python v3.8.5)
5. Processing of pySCENIC output (R v3.6.1)

Data availability

The gene count matrix and metadata table are available for download at: https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x

All datasets used in the code are available for download in the following Zenodo repository: https://doi.org/10.5281/zenodo.5729701