scrna-analysis

Author: Pengcen Jiang, Benjie Miao

Course: DSC 244: Large-Scale Statistical Analysis, WI25@UCSD

Instructor: Dr. Armin Schwartzman

Single cell RNA sequence analysis for the public dataset from Allen Brain Cell Atlas link

Instructions

Packages required in python 3 environment:

• numpy
• pandas
• scanpy
• statsmodels
• anndata
• scipy
• shap
• matplotlib
• matplotlib-venn

Run 'data_download.ipynb' to download 'abc_atlas_access' package and all the data under analysis.

Run 'age_related_genes_analysis.ipynb' to go through the analysis for detecting aging-related genes.

Run 'gender_ageDE_analysis.ipynb' to go through the analysis for gender-specific aging-related gene expression analysis.

Reference

[1] Jin, Kelly, et al. "Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice." Nature (2025): 1-15.