Orange3-Bioinformatics

Release v4.0.1.dev9+g267c7dd.

https://pepy.tech/badge/orange3-bioinformatics https://img.shields.io/pypi/l/orange3-bioinformatics.svg

Bioinformatics add-on for Orange data mining software package.

Description

Orange Bioinformatics extends Orange, a data mining software package, with common functionality for bioinformatics. The provided functionality can be accessed as a Python library or through a visual programming interface (Orange Canvas). The latter is also suitable for non-programmers.

In Orange Canvas the analyst connects basic computational units, called widgets, into data flow analytics schemas. Two units-widgets can be connected if they share a data type. Compared to other popular tools like Taverna, Orange widgets are high-level, integrated potentially complex tasks, but are specific enough to be used independently. Even elaborate analyses rarely consist of more than ten widgets; while tasks such as clustering and enrichment analysis could be executed with up to five widgets. While building the schema each widget is independently controlled with settings, the settings do not conceptually burden the analyst.

Orange Bioinformatics provides access to publicly available data, like GEO data sets, GO and KEGG. All features can be combined with powerful visualization, network exploration and data mining techniques from the Orange data mining framework.

Installation

To install the add-on with pip use

pip install Orange3-bioinformatics

To register this add-on with Orange, but keep the code in the development directory (do not copy it to Python’s site-packages directory), run

pip install -e .

Documentation / widget help can be built by running

make html htmlhelp

from the doc directory.

Usage

After the installation, the widgets from this add-on are registered with Orange. To run Orange from the terminal, use

python3 -m Orange.canvas

or

orange-canvas

The new widgets are in the toolbox bar under Bioinformatics section.

Content

Please see Contents for full documentation