Orange Bioinformatics documentation
===================================

Orange Bioinformatics is an add-on for Orange_ data mining software package. It
extends Orange by providing functionality for some elementary tasks in
bioinformatics, like gene set analysis, enrichment, and access to pathway
libraries. Included are also widgets for with graphical user interface
for, mainly, gene expression analytics.

.. _Orange: http://orange.biolab.si/

Widgets
-------

.. toctree::
   :maxdepth: 1
 
   widgets/biomart
   widgets/databasesupdate
   widgets/dataprofiles
   widgets/dictyExpress
   widgets/differentialexpression
   widgets/expressionprofiledistances
   widgets/geneinfo
   widgets/genexpress
   widgets/geodatasets
   widgets/gobrowser
   widgets/keggpathways
   widgets/maplot
   widgets/PIPAx
   widgets/qualitycontrol
   widgets/selectgenes
   widgets/setenrichment
   widgets/volcanoplot

Scripting Reference
-------------------
   
.. toctree::
   :maxdepth: 1

   reference/arrayexpress.rst
   reference/biomart.rst
   reference/dicty.rst
   reference/dictybase.rst
   reference/gene.rst
   reference/gene.homology.rst
   reference/genesets.rst
   reference/geo.rst
   reference/go.rst
   reference/gsea.rst
   reference/kegg.rst
   reference/omim.rst
   reference/ontology.rst
   reference/ppi.rst
   reference/taxonomy.rst
   reference/utils.stats.rst

Installation
------------

To install Bioinformatics add-on for Orange from PyPi_ run::

    pip install Orange-Bioinformatics

To install it from source code run::

    python setup.py install

To build Python egg run::

    python setup.py bdist_egg

To install add-on in `development mode`_ run::

    python setup.py develop

.. _development mode: http://packages.python.org/distribute/setuptools.html#development-mode
.. _PyPi: http://pypi.python.org/pypi

Source Code and Issue Tracker
-----------------------------

Source code is available on Bitbucket_. For issues and wiki we use Trac_.

.. _Bitbucket: https://bitbucket.org/biolab/orange-bioinformatics
.. _Trac: http://orange.biolab.si/trac/

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`