README.md

About

Effect of APOE Alleles on the Glial Transcriptome in Normal Aging and Alzheimer's Disease

We investigated the differential effects of APOE alleles on the microglia and astrocyte transcriptome in the absence and presence of neuritic plaques (NPs) using bulk brain RNA-seq data from two large brain banks and performed follow-on experiments in APOE knock-in mice.

Setup

Install R to run our code.

Documentation

To read our documented code, please visit mindds.github.io/apoe-glia or see below.

Functions

• Models
• Spectral Clustering

ROSMAP

• Define Variables
• Pre-Process Data
• Microglia Analysis
• Astrocyte Analysis

MSBB

• Define Variables
• Merge Data
• Microglia Analysis

qPCR Analysis

• qPCR Analysis

Code Availability

Our full codebase is available for download on GitHub.