Metadata-Version: 2.1
Name: pycoMeth
Version: 0.4.5
Summary: DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
Home-page: https://github.com/a-slide/pycoMeth
Author: Adrien Leger
Author-email: aleg@ebi.ac.uk
License: GPL
Description: ![pycoMeth](./docs/pictures/pycoMeth_long.png)
        
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        ---
        
        **Full documentation is available at https://a-slide.github.io/pycoMeth/**
        
        ---
        
        **DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets**
        
        `pycoMeth` can be used for further analyses starting from the output files generated by [`Nanopolish call-methylation`](https://github.com/jts/nanopolish). The package contains a suite of tools to **find CpG islands** calculate the **methylation probability at CpG dinucleotide or CpG island resolution** across the entire genome and to perform a **simple differential methylation analysis** across multiple samples.
        
        `pycoMeth` generates extensive tabulated reports and BED files which can be loaded in a genome browser. However, this is not a visualisation tool *per se*. An excellent complementary tool to visualise and explore methylation status for specific loci is [`Methplotlib`](https://github.com/wdecoster/methplotlib) developed by [Wouter de coster](https://twitter.com/wouter_decoster).
        
        Please be aware that `pycoMeth` is a research package that is still under development. The API, command line interface, and implementation might change without retro-compatibility.
        
        ---
        
        ### pycoMeth workflow
        
        ![Workflow](docs/pictures/pycoMeth_package.png)
        
        ### pycoMeth example output IGV rendering
        
        ![IGV](docs/pictures/pycoMeth_all.png)
        
        ### pycoMeth example HTML report
        
        [Example HTML report](https://a-slide.github.io/pycoMeth/Comp_Report/medaka_html/pycoMeth_summary.html)
        
        ![HTML](docs/pictures/pycoMeth_HTML.gif)
        
        ---
        
        ### Citing
        
        The repository is archived at Zenodo. If you use `pycoMeth` please cite as follow:
        
        Adrien Leger. (2020, January 28). a-slide/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.3629254
        
        ## Authors and contributors
        
        * Adrien Leger (@a-slide) - aleg {at} ebi.ac.uk
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.6
Description-Content-Type: text/markdown
