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
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