Metadata-Version: 2.4
Name: cpgtools
Version: 3.0.0
Summary: Python tools for DNA methylation analysis, imputation, epigenetic clocks, and cell-type deconvolution.
Author-email: Liguo Wang <wangliguo78@gmail.com>
License-Expression: MIT
Keywords: dna methylation,epigenetics,epigenetic clock,cell deconvolution,450K,EPIC,RRBS,WGBS
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: numpy>=1.23
Requires-Dist: scipy>=1.9
Requires-Dist: pandas>=1.5
Requires-Dist: scikit-learn>=1.3
Requires-Dist: matplotlib>=3.7
Requires-Dist: umap-learn>=0.5
Requires-Dist: bx-python>=0.11
Requires-Dist: weblogo>=3.7
Requires-Dist: pycombat>=0.20
Dynamic: license-file

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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:

```bash
pip install cpgtools
```

Or install the latest development version from GitHub:

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

### (Optional) Create a virtual environment

Using a virtual environment is recommended but not required.

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

## Upgrade

```bash
pip install --upgrade cpgtools
```

## Uninstall

```bash
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
