alzGPSnet

Multimodal single-cell/nucleus RNA-sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer’s disease

Code

• GPSnet_module_generation.py Python implementation of GPSnet algorithm https://github.com/ChengF-Lab/GPSnet
• Grubman_EC_altas.R is single cell analysis code for the data from the paper <A single-cell altas of entorhinal cortex from individuals with Alzheimer's disease revelas cell-type-specific gene expression regulation>
• Leng_EC_Astrocyte.R is single cell analysis code for the data from the paper <Molecular characterization of selectively vulnerable neurons in Alzheimer’s Disease>

Requirements

• Python 3.7 (numpy, scipy)
• R 4.0.3. (ggplot2, dplyr, Seurat, scater, DropletUtils, BiocSingular, scran, patchwork, grid, cowplot, BRETIGEA, Matrix, rray,and MAST)