Metadata-Version: 2.1
Name: pycoMeth
Version: 2.2.1rc1
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
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
License-File: LICENSE

![pycoMeth](./docs/pictures/pycoMeth_long.png)

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---
Version in this branch: 2.2.1rc1

---

**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 pycometh

Or using pip:
    
    pip install pycometh

---

### 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)


