For bulk RNA-seq data from rat brain, we will use single cell RNA-seq data from mouse PFC to estimate cell-type fractions. We will use the popular Dampened Weighted Least Squares method in R.

Starting with raw counts with Rat Ensembl Gene IDs, filtering, normalizing, and annotating the reads prior to PCA with data plotting and writing results to file.

Build clusters from highly correlated adjacent epigenetic marks from sequencing data.This applies to studies examining DNA methylation, ChIP-seq histone marks, and ATAC-seq open chromatin regions. The strength of these clusters can then be compared between control and treatment groups. This is an example using ATAC-seq data.

Iterate through all genes to test mediation effects using the mediation R package