CpGtools

CpGtools is a Python package for analyzing DNA methylation data generated from Illumina Infinium arrays and sequencing-based methylation assays. It provides tools for data preprocessing, quality control, imputation, epigenetic clock estimation, deconvolution, and downstream analysis.

Features

• Read and preprocess DNA methylation matrices
• Missing-value imputation
• DNA methylation age estimation (epigenetic clocks)
• Cell-type deconvolution
• Differential methylation analysis
• Data visualization

Installation

Install the latest stable release from PyPI:

pip install cpgtools

Or install the latest development version from GitHub:

pip install git+https://github.com/liguowang/cpgtools.git

(Optional) Create a virtual environment

Using a virtual environment is recommended but not required.

python3 -m venv cpgtools-env
source cpgtools-env/bin/activate

Upgrade

pip install --upgrade cpgtools

Uninstall

pip uninstall -y cpgtools

Documentation

Documentation is available at:

https://cpgtools.readthedocs.io/

Source Code

https://github.com/liguowang/cpgtools

License

CpGtools is distributed under the MIT License.

Citation

If you use CpGtools in your research, please cite:

Wei T, Nie J, Larson NB, Ye Z, Eckel-Passow JE, Robertson KD, Kocher J-P, Wang L. CpGtools: a python package for DNA methylation analysis. Bioinformatics. 2021;37(11):1598–1599. DOI: https://doi.org/10.1093/bioinformatics/btz916 PMID: 31808791