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, Biomart, GO, KEGG, Atlas, ArrayExpress, and PIPAx database. As for the analytics, there is gene selection, quality control, scoring distances between experiments with multiple factors. All features can be combined with powerful visualization, network exploration and data mining techniques from the Orange data mining framework.

Documentation: http://orange-bioinformatics.readthedocs.org/

Orange Model Maps is an add-on for Orange data mining software package. It extends Orange by providing modules for building model maps. It also provides widgets for Orange Canvas to enable users explore model maps.

Documentation is found at:

http://orange-modelmaps.readthedocs.org/

Orange Multitarget is an add-on for Orange data mining software package. It extends Orange by providing methods that allow for classification of datasets with multiple classes.

Currently supported techniques:

• Binary Relevance
• Classifier Chains and Ensemble Classifier Chains
• Clustering Trees
• Neural Networks
• Partial Least Squares

Documentation can be viewed at:

http://orange-multitarget.readthedocs.org/

Orange Network is an add-on for Orange data mining software package. It provides network visualization and analysis tools.

Documentation is found at:

http://orange-network.readthedocs.org/

Orange NMF is an add-on for Orange data mining software package. It provides non-negative matrix factorization algorithms (NMF) through NIMFA and robust singular value decomposition (rSVD). It includes widgets that deal with missing data in input matrices, their normalizations, viewing and assessing the quality of matrix factors returned by different matrix factorization algorithms.

Documentation is found at:

https://orange-nmf.readthedocs.org

Widgets were designed and implemented by Fajwel Fogel (Ecole Polytechnique ParisTech). All NMF methods call NIMFA library, implemented by Marinka Zitnik (Bioinformatics Laboratory, FRI UL). Thanks also to Doug Marsteller, Stan Young (NISS), Chris Beecher, Paul Fogel.

Orange Reliability is an add-on for Orange data mining software package. It extends Orange by providing functionality to estimate reliability of individual regression and classification predictions.

Documentation can be found at:

http://orange-reliability.readthedocs.org/

Orange Text Mining is an add-on for Orange data mining software package. It extends Orange by providing common functionality for basic tasks in text mining.

Documentation is found at:

http://orange-text.readthedocs.org/