source: orange-bioinformatics/docs/rst/index.rst @ 2064:b7a3d649f5ee

Revision 2064:b7a3d649f5ee, 1.8 KB checked in by markotoplak, 3 days ago (diff)

Added ppi, biomart and arrayexpress to docs (from docstrings).

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1Orange Bioinformatics documentation
2===================================
3
4Orange Bioinformatics is an add-on for Orange_ data mining software package. It
5extends Orange by providing functionality for some elementary tasks in
6bioinformatics, like gene set analysis, enrichment, and access to pathway
7libraries. Included are also widgets for with graphical user interface
8for, mainly, gene expression analytics.
9
10.. _Orange: http://orange.biolab.si/
11
12Widgets
13-------
14
15.. toctree::
16   :maxdepth: 1
17 
18   PIPA.rst
19   databases.rst
20   geodatasets.rst
21
22Scripting Reference
23-------------------
24   
25.. toctree::
26   :maxdepth: 1
27
28   reference/arrayexpress.rst
29   reference/biomart.rst
30   reference/dicty.rst
31   reference/dictybase.rst
32   reference/gene.rst
33   reference/gene.homology.rst
34   reference/genesets.rst
35   reference/geo.rst
36   reference/go.rst
37   reference/gsea.rst
38   reference/kegg.rst
39   reference/omim.rst
40   reference/ontology.rst
41   reference/ppi.rst
42   reference/taxonomy.rst
43   reference/utils.stats.rst
44
45Installation
46------------
47
48To install Bioinformatics add-on for Orange from PyPi_ run::
49
50    pip install Orange-Bioinformatics
51
52To install it from source code run::
53
54    python setup.py install
55
56To build Python egg run::
57
58    python setup.py bdist_egg
59
60To install add-on in `development mode`_ run::
61
62    python setup.py develop
63
64.. _development mode: http://packages.python.org/distribute/setuptools.html#development-mode
65.. _PyPi: http://pypi.python.org/pypi
66
67Source Code and Issue Tracker
68-----------------------------
69
70Source code is available on Bitbucket_. For issues and wiki we use Trac_.
71
72.. _Bitbucket: https://bitbucket.org/biolab/orange-bioinformatics
73.. _Trac: http://orange.biolab.si/trac/
74
75Indices and tables
76==================
77
78* :ref:`genindex`
79* :ref:`modindex`
80* :ref:`search`
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