Metadata-Version: 2.4
Name: marine-omics
Version: 0.1.3
Summary: Utilities for metagoflow and marine omics demos
Maintainer-email: FAIR-Ease <dpalecek@ualg.pt>
Keywords: marine omics,emo-bon,metagenomics,bioinformatics,data visualization,data analysis
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bioblend>=1.4.0
Requires-Dist: bokeh>=3.7.3
Requires-Dist: holoviews>=1.20.0
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Dynamic: license-file

# marine-omics

[![Python Version](https://img.shields.io/pypi/pyversions/momics.svg?color=green)](https://python.org)
![PyPI - Version](https://img.shields.io/pypi/v/marine-omics)
[![Read the Docs](https://img.shields.io/readthedocs/marine-omics)](https://marine-omics-methods.readthedocs.io/en/latest/)
[![tests](https://github.com/palec87/marine-omics/workflows/tests/badge.svg)](https://github.com/palec87/marine-omics/actions)
[![codecov](https://codecov.io/gh/emo-bon/marine-omics-methods/branch/main/graph/badge.svg)](https://codecov.io/gh/emo-bon/marine-omics-methods)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

Package of utilities for FAIR-Ease demo workflows.

These methods are currently use only for FAIR-EASE [pilot demos](https://github.com/palec87/momics-demos), but eventually they can serve for general purpose manipulation of metagenomic data, locally and in VREs.

The idea is to provide testable methods to allow as much flexibility and remixing of the functionalities provided

## European Marine Omics Biodiversity Observation Network

Specifically, we aim primarily to manipulate EMO-BON marine genomics sampling data and metadata from ENA project [PRJEB51688](https://www.ebi.ac.uk/ena/browser/view/PRJEB51688). The interactive dashboards and jupyter notebooks built on top of this repository can be found [here](https://github.com/emo-bon/momics-demos/tree/main).

The methods are mixture of statistical methods, plotting functionalities, metadata and data handling utilities and generators of `holoviz panel` widgets and panes. Experimental integration to `Galaxy` uses a wrapper around [bioblend](https://bioblend.readthedocs.io/en/latest/).
