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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.

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
• Significantly faster compared to minfi and conumee2.
• Methylation analysis tool with a graphical browser interface for UMAP analysis, CNV plots and supervised classification
  • Can be run from the command line with minimal setup or customized through a Python script

Documentation

The mepylome documentation, including installation instructions, tutorial and API, is available at https://mepylome.readthedocs.io/

Usage

Methylation extraction and copy number variation plots

from pathlib import Path

from mepylome import CNV, MethylData

# Sample
analysis_dir = Path("/path/to/idat/directory")
sample_file = analysis_dir / "200925700125_R07C01"

# CNV neutral reference files
reference_dir = Path("/path/to/reference/directory")

# Get methylation data
sample_methyl = MethylData(file=sample_file)
reference_methyl = MethylData(file=reference_dir)

# Beta value
betas = sample_methyl.betas

# Print overview of processed data
print(sample_methyl)

# CNV anylsis
cnv = CNV.set_all(sample_methyl, reference_methyl)

# Visualize CNV in the browser
cnv.plot()

Methylation analysis: Command-line interface and GUI

Basic usage:

Mepylome provides a command-line interface for launching a GUI and performing methylation analysis. Ensure you have an analysis directory, a CNV reference directory, and an annotation file (located within the analysis directory). Use the following command to initiate the analysis:

mepylome --analysis_dir /path/to/idats --reference_dir /path/to/ref

If you want to perform a quick test, use:

mepylome --tutorial

This command downloads sample IDAT files and provides a demonstration of the package's functionality.

See https://mepylome.readthedocs.io/ for details.

C++ parser

Mepylome also includes a C++ parser. See https://mepylome.readthedocs.io/ for details.

Contributing

Contributions are welcome! If you have any bug reports, feature requests, or suggestions, please open an issue or submit a pull request.

License

This project is licensed under the GPL-3.0 license.

Acknowledgements

Mepylome is strongly influenced by minfi and conumee2. Some functionalities, such as the manifest handler and parser, are adapted from methylprep.