Metadata-Version: 2.1
Name: pycoMeth
Version: 2.2.2
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: 2.2.2
        
        ---
        
        **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.
        
        ---
        ### Installation
        
        Install either using conda:
        
            conda install -c snajder-r -c bioconda -c conda-forge pycometh
        
        Or using pip:
            
            pip install pycometh
        
        ### Documentation
        
        A more detailed usage documentation can be found at https://snajder-r.github.io/pycoMeth/
        
        ### pycoMeth workflow
        
        ![Workflow](https://snajder-r.github.io/pycoMeth/images/overview.svg)
        
        
        ### pycoMeth example HTML report
        
        [Example HTML report 1](https://snajder-r.github.io/pycoMeth/examples/pycometh_report1.html)
        
        [Example HTML report 2](https://snajder-r.github.io/pycometh/examples/pycometh_report2.html)
        
        ---
        
        ### Citing
        
        The repository is archived at Zenodo. https://doi.org/10.5281/zenodo.6637645
        
        If you find pycoMeth useful, please cite our preprint:
        
        Snajder, Rene H., Oliver Stegle, and Marc Jan Bonder. 2022. "PycoMeth: A Toolbox for Differential Methylation Testing from Nanopore Methylation Calls." bioRxiv. https://doi.org/10.1101/2022.02.16.480699.
        
        
            @article {Snajder2022.02.16.480699,
                author = {Snajder, Rene and Leger, Adrien and Stegle, Oliver and Bonder, Marc Jan},
        	    title = {pycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls},
        	    year = {2022}, doi = {10.1101/2022.02.16.480699}, publisher = {Cold Spring Harbor Laboratory},
                journal = {bioRxiv}
            }
        
        
        ### Authors
        
        * Rene Snajder (rene.snajder@gmail.com)
        * Adrien Leger
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown
