Deconvolving brain cell-type proportions (brain CTP) from DNA methylation data.
This repo contains code for:
Brain cell-type shifts in Alzheimer’s disease, autism and schizophrenia interrogated using methylomics and genetics Chloe X Yap, Daniel D Vo, Matthew Heffel, Arjun Bhattacharya, Cindy Wen, Yuanhao Yang, Kathryn E Kemper, Jian Zeng, Zhili Zheng, Zhihong Zhu, Eilis Hannon, Dorothea Seiler Vellame, Alice Franklin, Christa Caggiano, Brie Wamsley, Daniel H Geschwind, Noah Zaitlen, Alexander Gusev, Bogdan Pasaniuc, Jonathan Mill, Chongyuan Luo, Michael J Gandal. (2024)
deconvolution/: brain CTP deconvolution pipeline scripts
- Want to deconvolve your own bulk methylation array data (Illumina EPIC or 450K)?
- Jump right over here!
- This folder contains instructions and easy-to-use scripts and processed reference data (plus info on how we got there)
qc/: methylation and genotyping QC scripts
analysis/: scripts used for analysis
- Where possible, we've tried to keep data within this GitHub repo
- However, for larger files we've used Zenodo [DOI 10.5281/zenodo.7604233], but this is all described in the README within the relevant folders :)