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        "author": "Kathy Chen",
        "author_email": "chen.kathleenm@gmail.com",
        "bugtrack_url": null,
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            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "Crosstalk correction\n--------------------\nPython 3 implementation of `Donato et al.'s 2013 maximum impact estimation\nalgorithm <http://doi.org/10.1101/gr.153551.112>`_\nfor correcting crosstalk effects in pathway analysis.\n\nThis code has been tested on Python 3.5.\n\nBackground\n----------\n\n**Crosstalk**: Donato et al. (2013) use the term crosstalk to refer to the\neffect that pathways exercise on each other (in pathway analysis methods\nsuch as enrichment analysis, functional class scoring, and topology-based\nmethods) due to the presence of overlapping genes.\n\n**Maximum impact estimation**: They developed a correction method called\nmaximum impact estimation that takes into account overlaps between pathways.\nThe approach infers an underlying pathway impact matrix where each gene\nonly contributes to one pathway using an expectation maximization technique.\n\n**PathCORE-T**: The crosstalk correction method is used in the PathCORE-T\nsoftware, a hypothesis generation tool that identifies co-occurring pathways\nfrom the results of an unsupervised analysis of transcriptomic data. Due to\nconfusion around the term \"crosstalk,\" we refer to this procedure as\n\"gene overlap correction\" in the PathCORE-T software and paper.\n\nInstallation\n----------------\nTo install the current PyPI version (recommended), run::\n\n    pip install crosstalk-correction\n\nFor the latest GitHub version, run::\n\n    pip install git+https://github.com/kathyxchen/crosstalk-correction.git#egg=crosstalk-correction\n\nExamples\n--------\nThe `crosstalk_correction` method is used in `PathCORE-T <https://github.com/greenelab/PathCORE-T>`_\n(see: `feature_pathway_overrepresentation <https://github.com/greenelab/PathCORE-T/blob/master/pathcore/feature_pathway_overrepresentation.py#L86>`_)\n\nA visualization of what crosstalk correction does in the context of the PathCORE-T analysis\ncan be viewed `here <https://github.com/greenelab/PathCORE-T-analysis/blob/master/jupyter-notebooks/Figure3_overlap_correction.ipynb>`_.\n\nFor more details, please see the `PathCORE-T pre-print <http://biorxiv.org/content/early/2017/06/08/147645>`_.\n\nPackage contents\n----------------\n\n=======================\ncrosstalk_correction.py\n=======================\ncrosstalk_correction.py contains the implementation of the crosstalk\ncorrection procedure. The method ``crosstalk_correction`` wraps\nthe maximum impact estimation algorithm (method ``maximum_impact_estimation``)\nand reduces the number of pre/post-processing steps required to\nrun/interpret the results of ``maximum_impact_estimation``.\n\nWe recommend that the method ``crosstalk_correction`` be used directly\nin most use cases.\n\nFor applications of maximum impact estimation that are not covered by\nthis method, the following methods have also been made public\nand can be imported:\n\n- ``maximum_impact_estimation``\n- ``initialize_membership_matrix``\n- ``index_element_map``\n\nAcknowledgements\n----------------\nThis work was supported by the Penn Institute for Bioinformatics",
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