README.md

In neurogenomics/CHAS: Cell type deconvolution of bulk tissue histone acetylomes from epigenetic data

Cell type-specific Histone Acetylation Score (CHAS)

Cell type deconvolution of bulk brain H3K27ac profiles

Kitty Murphy, Yuqian Ye, Alexi Nott, and Sarah Marzi

Introduction

Cell type identity is a major driver of epigenetic variation, making biological interpretation of bulk tissue epigenomes difficult. Here we present CHAS (cell type-specific histone acetylation score), an R package for the cell deconvolution of bulk brain H3K27ac profiles. CHAS is split into two independent algorithms. In the first, CHAS annotates peaks identified in bulk brain studies of H3K27ac to cell type-specific signals in four major brain cell types, and based on normalised signal intensities generates cell type-specific histone acetylation scores to act as a proxy for cell type proportion. In the second, CHAS implements non-negative matrix factorisation based on the RNA-seq cell deconvolution tool EPIC, to estimate cell type proportions within bulk H3K27ac samples.

If you use CHAS, please cite our preprint: Murphy, Nott & Marzi. CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders. bioRxiv, 2021.

Tutorial

See the CHAS vignette website for up-to-date instructions on usage.

CHAS workflow

Citation

• If you use CHAS, please cite our preprint: Murphy, Nott & Marzi. CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders. bioRxiv, 2021.
• If you use the cell sorted H3K27ac data associated with this package then please cite the following paper: Nott, et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science, 2019.
• If you use the entorhinal cortex peaks and/or counts available within this package then please cite the following paper: Marzi, et al. A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex. Nature Neuroscience, 2018.

Installing CHAS

if (!require("remotes")) {
  install.packages("remotes")
}
remotes::install_github("Marzi-Lab/CHAS")

You can then load the package and data package:

library(CHAS)

License

This project is licensed under the terms of the GNU General Public License v3.0.

neurogenomics/CHAS documentation built on Jan. 20, 2025, 4:03 p.m.