kundajelab/alzheimers_parkinsons

Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis

Jupyter Notebook

Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease

https://www.biorxiv.org/content/10.1101/2020.01.06.896159v1

Bulk ATAC-seq data processing / peak calling

Differential accessibility analysis with DESeq2 and limma voom

Single-cell ATAC-seq data processing / peak calling

LD score regression: Cell type specific analyses

Colocalization analysis

SVM model training

SNP effect scoring with SVMs

SNP effect interpretation

Neural network training

Neural network interpretation/ variant score visualization