Welcome to pylluminator

Tutorials | API documentation | Source code | Release on pip

Pylluminator is a Python package designed to provide an efficient workflow for processing, analyzing, and visualizing DNA methylation data. Pylluminator is inspired from the popular R packages SeSAMe and ChAMP.

Pylluminator supports the following Illumina’s Infinium Beadchip array versions:

human: 27k, 450k, MSA, EPIC, EPIC+, EPICv2
mouse: MM285
mammalian: Mammal40

Main functionalities

idat files parsing
data preprocessing
- Type-I probes channel inference
- Dye bias correction (3 methods: using normalization control probes / linear scaling / non-linear scaling)
- Detection p-value calculation (pOOBAH)
- Background correction (NOOB)
- Batch effect correction (ComBat)
data analysis and visualisation
- beta values (density, PCA, MDS, dendrogram…)
- DMPs accounting for replicates / random effects, DMRs
- CNV, CNS
- pathway analysis with GSEApy (GSEA, ORA)
quality control

Visualization examples:

Fig 1. Samples beta values density	Fig 2. Differentially methylated regions (DMRs)
Fig 3. Probes beta values associated with a specific gene	Fig 4. Copy number variations (CNVs)

Installation

With pip

You can install Pylluminator directly with:

pip install pylluminator

From source

We recommend using a virtual environment with Python 3.12 to build pylluminator from source. Here is an example using Conda.

Setup the virtual environment (optional)

If you don’t have Conda installed yet, here are the instructions depending on your OS : Windows | Linux | MacOS. After installing it, make sure you have Pip installed by running the following command in the terminal:

conda install anaconda::pip

Now you can create a Conda environment named “pylluminator” and activate it. You can change the name to your liking ;)

conda create -n pylluminator python=3.12
conda activate pylluminator

Install pylluminator

You can download the latest source from github, or clone the repository with this command:

git clone https://github.com/eliopato/pylluminator.git

Your are now ready to install the dependencies and the package :

cd pylluminator
pip install -r requirements.txt

Usage

Refer to https://pylluminator.readthedocs.io/ for step-by-step tutorials and detailed documentation.

Contributing

We welcome contributions! If you’d like to help improve the package, please follow these steps:

Fork the repository.
Create a new branch for your feature or bugfix.
Make your changes and test them.
Submit a pull request describing your changes.

Bug reports / new features suggestion

If you encounter any bugs, have questions, or feel like the package is missing a very important feature, please open an issue on the GitHub Issues page.

When opening an issue, please provide as much detail as possible, including:

Steps to reproduce the issue
The version of the package you are using
Any relevant code snippets or error messages

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgements

This package is strongly inspired from SeSAMe and includes code from methylprep for .idat files parsing.