Metadata-Version: 2.1
Name: MethylVerse
Version: 1.0.2
Summary: Python package for methylation data
Home-page: https://github.com/kylessmith/MethylVerse
License: GPL-2.0-or-later
Keywords: WGBS,450k,850k,EPIC,methylation
Author: Kyle S. Smith
Author-email: kyle.smith@stjude.org
Maintainer: Kyle S. Smith
Maintainer-email: kyle.smith@stjude.org
Requires-Python: >=3.10
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
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Requires-Dist: bokeh (>=3.1.0,<4.0.0)
Requires-Dist: cython (>=3.0.0,<4.0.0)
Requires-Dist: h5py (>=3.12.1)
Requires-Dist: joblib (>=1.4.2)
Requires-Dist: linear_segment (>=1.2.1,<2.0.0)
Requires-Dist: matplotlib (>=3.7.1,<4.0.0)
Requires-Dist: numpy (>=1.23.5)
Requires-Dist: onnxruntime (>=1.20.0)
Requires-Dist: pandas (>=2.0.0,<3.0.0)
Requires-Dist: pysam (>=0.22.0)
Requires-Dist: scikit-learn (>=1.2.2)
Requires-Dist: scikit-network (>=0.33.0)
Requires-Dist: scipy (>=1.9.1)
Requires-Dist: seaborn (>=0.12.2)
Requires-Dist: statsmodels (>=0.14.0)
Project-URL: Documentation, https://www.biosciencestack.com/static/MethylVerse/docs/index.html
Project-URL: Repository, https://github.com/kylessmith/MethylVerse
Description-Content-Type: text/markdown

# MethylVerse

[![Build Status](https://travis-ci.org/kylessmith/MethylVerse.svg?branch=master)](https://travis-ci.org/kylessmith/MethylVerse) [![PyPI version](https://badge.fury.io/py/MethylVerse.svg)](https://badge.fury.io/py/MethylVerse)
[![Coffee](https://img.shields.io/badge/-buy_me_a%C2%A0coffee-gray?logo=buy-me-a-coffee&color=ff69b4)](https://www.buymeacoffee.com/kylessmith)

<img src="MethylVerse_logo.png" width="300" />
Library to work with WGBS, EM-seq, and/or methylation array data in one interface.


For full usage and installation [documentation][methylverse_docs]

## Install

If you dont already have numpy and scipy installed, it is best to download
`Anaconda`, a python distribution that has them included.  
```
    https://continuum.io/downloads
```

Dependencies can be installed by:

```
    pip install -r requirements.txt
```

PyPI install, presuming you have all its requirements installed:
```
    pip install methylverse
```

## Quick start

Test numpy random integers:

```python
import MethylVerse as mv

beta_values = mv.core.read_methylation("path/to/methylation")

```

Run the M-PACT classifier from the cammandline
```
python -m MethylVerse MPACT example.bedgraph --impute --regress --call_cnvs --verbose
```


[methylverse_docs]: https://www.biosciencestack.com/static/MethylVerse/docs/index.html
