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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

Key dates

PyPI data
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  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for liguow from gravatar.com liguow

Credits

Author: Liguo Wang

License expression

MIT
View SPDX License List

Requires

Python >=3.9

Tags

dna methylation epigenetics epigenetic clock cell deconvolution 450K EPIC RRBS WGBS

Classifiers

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