---

Mepylome: Methylation Array Analysis Toolkit

Mepylome is an efficient Python toolkit tailored for parsing, processing, and analyzing methylation array IDAT files. Serving as a versatile library, Mepylome supports a wide range of methylation analysis tasks. It also includes an interactive GUI that enables users to generate UMAP plots and CNV plots (Copy Number Variation) directly from collections of IDAT files.

Mepylome is open source, and hosted at github: https://github.com/brj0/mepylome

Publication

This library is described in the following peer-reviewed publication:

https://doi.org/10.1002/aisy.202500778

Features

• Parsing of IDAT files

• Extraction of methylation signals

• Calculation of Copy Number Variations (CNV) with visualization using plotly

• Support for the following Illumina array types: 450k, EPIC, EPICv2, MSA48

• Significantly faster compared to minfi and conumee2

• Methylation analysis tool with a graphical browser interface for UMAP analysis and CNV plots

  • Can be run from the command line with minimal setup or customized through a Python script

• CN-summary plots

Documentation outline

1. Installation instructions

2. The GUI, recommended for all new users

3. The tutorial, recommended for all new users

Contents:

• Installation
  • From PyPI
  • From Source
  • CNV Segments
  • Uninstallation
  • Platform Compatibility
• User Guide: CLI / GUI
  • Graphical user interface: Quick demonstration
  • General Setup
  • Comand line interface
• Tutorial (library)
  • Setup
  • Parsing IDAT files
  • Manifest files
  • RawData
  • MethylData
  • Copy number variation (CNV)
  • Methylation Analysis
  • Supervised Classification
• Performance
  • Overview
  • Performance Comparison
  • How It Works
• API Reference
  • mepylome.dtypes.idat
  • mepylome.dtypes.manifests
  • mepylome.dtypes.beads
  • mepylome.dtypes.cnv
  • mepylome.analysis.methyl
  • mepylome.analysis.methyl_aux
  • mepylome.analysis.methyl_clf

Indices and tables

• Index

• Module Index

• Search Page