Metadata-Version: 2.1
Name: pycoMeth
Version: 2.0.0
Summary: Differential methylation calling suite for Nanopore methylation calls PycoMeth
Home-page: https://github.com/snajder-r/pycoMeth,
Author: Rene Snajder
Author-email: r.snajder@dkfz-heidelberg.de
License: GPL
Description: ![pycoMeth](./docs/pictures/pycoMeth_long.png)
        
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        ---
        Version in this branch: 2.0.0
        
        ---
        
        **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**, **segment methylome**, and to perform a **differential methylation analysis** across multiple samples.
        
        `pycoMeth` generates extensive tabulated reports and BED files which can be loaded in a genome browser. In addition, an interactive HTML report of differentially
        methylated intervals/islands can also generated at the end of the analysis.
        
        [`Methplotlib`](https://github.com/wdecoster/methplotlib) developed by [Wouter de coster](https://twitter.com/wouter_decoster) is an excellent complementary tool to visualise and explore methylation status for specific loci.
        
        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 1](https://a-slide.github.io/pycoMeth/Comp_Report/medaka_html/pycoMeth_summary_report.html)
        
        [Example HTML report 2](https://a-slide.github.io/pycoMeth/Comp_Report/human_html/pycoMeth_summary_report.html)
        
        ![HTML](docs/pictures/pycoMeth_HTML.gif)
        
        ---
        
        ### Citing
        
        The repository is archived at Zenodo. If you use `pycoMeth` version 2, please cite as follow:
        
        Rene Snajder. (2021, May 18). snajder-r/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.4772051
        
        For version 1, please cite as:
        
        Adrien Leger. (2020, January 28). a-slide/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.3629254
        
        ## Authors and contributors
        
        * Rene Snajder (@snajder-r): rene.snajder@dkfz-heidelberg.de
        * Adrien Ledger (@a-slide)
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
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: >=3.7
Description-Content-Type: text/markdown
