kundajelab / alzheimers_parkinsons

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

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

scripts

Differential accessibility analysis with DESeq2 and limma voom

scripts

Single-cell ATAC-seq data processing / peak calling

scripts

LD score regression: Cell type specific analyses

scripts

Colocalization analysis

scripts

SVM model training

scripts

SNP effect scoring with SVMs

scripts

SNP effect interpretation

notebooks

Neural network training

scripts

Neural network interpretation/ variant score visualization

scripts

alzheimers_parkinsons's Issues

How can I get the input file from my atac data for these scripts?

Thank you very much for sharing the code. In fact, I read the code and I want to know how to get these input files. For example, how can I extract them from my ATAC data? thank you！

cell type annotation

Thank you for sharing the code!
I wonder how to get the cell type annotation and LSI matrix of processed data? I can not find it on either the GEO page or the scripts.