epi2hit

epi2hit is a Python package for integrative methylation / expression analysis and detection of epigenetically deregulated CpGs (eCpGs)

Features

• Filtering of probes to open chromatin using ATAC-seq peaks
• Mapping probes to genes
• Preliminary QC / filtering of probes
• Annotation with chromatin state (Pomerantz / chromHMM states)
• Correlation-based probe selection and duplicate resolution
• Annotation of probes with 3D chromatin loops
• Preparation of TCGA-like expression dictionaries
• Linear regression between methylation and expression
• Peak-based methylation categorisation and detection of eCpGs

All steps are available as individual functions, but they are designed to run in a simple end-to-end script or notebook.

Installation

pip install epi2hit