marine-omics

Package of utilities for FAIR-Ease demo workflows.

These methods are currently use only for FAIR-EASE pilot 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

Installation

One of the dependencies is currently not released to PyPI and is in active development, therefore you need to manually install it before marine-omics itself:

# UDAL data query layer
pip install git+https://github.com/fair-ease/py-udal-mgo.git

pip install marine-omics

European Marine Omics Biodiversity Observation Network

Specifically, we aim primarily to manipulate EMO-BON marine genomics sampling data and metadata from ENA project PRJEB51688. The interactive dashboards and jupyter notebooks built on top of this repository can be found here.

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.