Metadata-Version: 2.4
Name: epi2hit
Version: 0.1.2
Summary: Pipeline for integrative methylation / expression analysis and eCpG detection
Author: Daria Kiriy
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pyBigWig
Requires-Dist: seaborn
Requires-Dist: tqdm
Requires-Dist: matplotlib
Requires-Dist: scikit-learn
Requires-Dist: statannot
Requires-Dist: statsmodels
Requires-Dist: scipy
Requires-Dist: joblib
Requires-Dist: plotnine
Requires-Dist: pybedtools

# epi2hit

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

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## 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.

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## Installation

pip install epi2hit

