Metadata-Version: 2.4
Name: unduliner
Version: 1.0.0
Summary: CLI tool to link variants to methylation changes from nanopore data
Author-email: Halimat Chisom Atanda <gearthdexter@gmail.com>
License: MIT License
        
        Copyright (c) 2025 Halimat Chisom Atanda
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Source, https://github.com/Chisomgold/unduliner
Project-URL: Documentation, https://github.com/Chisomgold/unduliner/tree/main#unduliner
Keywords: genomics,bioinformatics,dna-methylation,variant-calling
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: torch
Requires-Dist: torch-summary
Requires-Dist: torchvision
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: pysam
Requires-Dist: bx-python
Requires-Dist: scikit-learn
Requires-Dist: scipy
Requires-Dist: numpy
Requires-Dist: pillow
Dynamic: license-file

Unduliner is a Python command-line tool for predicting whether genomic variants are associated with 
local DNA methylation changes using nanopore long-read sequencing data.

It integrates MM/ML-tagged BAM files, VCFs, and a pre-trained deep learning model to evaluate methylation 
differences around SNVs and structural variants.

Usage details and test data are available on the [Github page](https://github.com/Chisomgold/unduliner/tree/main)
