gelviz: A python python package for plotting genomic elements.

gelviz is a python package for plotting a wide range of genomic elements in a genome browser-like fashion. It comes with basic plotting functions that can be used for plotting different kind of genomic elements.

Example

The following example was created using published genomics and epigenomics data from 10.5281/zenodo.4557352. The data originates from the publication F. Haller, M. Bieg, R. Will, et al.. Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nature Communications volume 10, Article number: 368 (2019)

Please check the jupyter notebook for details on how the above figure was created.

Acknowledgements

This package was implemented during my time at the German Cancer Research Center in the group of Theoretical Bioinformatics headed by Prof. Dr. Roland Eils, where i was part of the core bioinformatics team of the Heidelberg Institute of Personalized Oncology (HIPO). Further refinment and final upload to PyPI was done during my time at Charite, Universitaetsmedizin Berlin, Berlin Institute of Health (BIH) in the Department of Digital Health headed by Prof. Roland Eils.

License

Copyright (c) 2021, Matthias Bieg

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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