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"info": {
"author": "Florian Wagner",
"author_email": "florian.wagner@duke.edu",
"bugtrack_url": null,
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"Intended Audience :: Developers",
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"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Programming Language :: Python :: 2.7",
"Topic :: Scientific/Engineering :: Bio-Informatics"
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"description": "..\n Copyright (c) 2016 Florian Wagner\n \n This file is part of pyAffy.\n \n pyAffy is free software: you can redistribute it and/or modify\n it under the terms of the GNU General Public License, Version 3,\n as published by the Free Software Foundation.\n \n This program is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU General Public License for more details.\n \n You should have received a copy of the GNU General Public License\n along with this program. If not, see .\n\npyAffy\n======\n\n.. \"|docs-latest| |docs-develop|\n\npyAffy is a Python/Cython implementation of the RMA algorithm for\nprocessing raw data from Affymetrix expression microarrays. For a detailed\ndiscussion of this implementation, see the `pyAffy PeerJ preprint`__. For\na list of changes, see the `changelog `_.\n\n__ peerj_preprint_\n\n.. _peerj_preprint: https://peerj.com/preprints/1790/\n\nInstallation\n------------\n\nOption 1: Using `pip`\n~~~~~~~~~~~~~~~~~~~~~\n\n.. code-block:: bash\n\n $ pip install pyaffy\n\n\nOption 2: Cloning the GitHub repository\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. code-block:: bash\n\n $ git clone https://github.com/flo-compbio/pyaffy.git\n $ cd pyaffy\n $ pip install -e .\n\nUsage\n-----\n\nThe `rma` function expects two parameters: A custom CDF file (from the\n`Brainarray web site`__) and an ordered dictionary (`collections.OrderedDict`)\nwith sample names as keys and corresponding CEL files as values.\n\n__ brainarray_\n\nThe `rma` function returns a list of genes, a list of samples, and an\nexpression matrix (of type `numpy.ndarray`), in that order.\n\n.. code-block:: python\n\n from pyaffy import rma\n # for documentation of the rma function, try:\n # help(rma)\n genes, samples, X = rma(cdf_file, sample_cel_files)\n\nA small `example with real code`__ is available in the `pyaffy-demos` repository.\n\n__ real_example_\n\n.. _brainarray: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp\n.. _real_example: https://github.com/flo-compbio/pyaffy-demos/tree/master/minimal\n\nCopyright and License\n---------------------\n\nCopyright (c) 2016 Florian Wagner\n\n::\n\n pyAffy is free software: you can redistribute it and/or modify\n it under the terms of the GNU General Public License, Version 3,\n as published by the Free Software Foundation.\n \n This program is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU General Public License for more details.\n \n You should have received a copy of the GNU General Public License\n along with this program. If not, see .",
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