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"description": "# PathwayAssessor\n\n- [Authors](#authors)\n- [Overview](#Overview)\n- [Installation](#installation)\n- [Usage](#usage)\n- [References](#references)\n- [Contributions](#contributions)\n\n## Authors\nBoris Reva1, Anna Calinawan1\n\n1Icahn School of Medicine at Mount Sinai (USA)\n\n## Overview\n\nComparison of tumors by activities of molecular pathways can help nominate disease driver pathways, \nidentify targets for therapeutic intervention, and determine clinically relevant subtypes and diagnostic biomarkers. \nWe introduce a new method for calculating overrepresentation and underrepresentation scores to assess a pathway\u2019s \nactivation and suppression, respectively.\nThe novelty of this approach is in independent assessment of overrepresentation and underrepresentation of pathway\u2019s \ngenes from both top and bottom of the ranked gene list of a given sample.\n\n\n## Installation\nRequires: Python >= 3.6\n\nTo install the latest version of PathwayAssessor, run:\n\n```\npip install pathway-assessor\n```\n\n## Usage\nTo see more information about the main functions, visit the [ReadMe included with the package code](https://github.com/annapamma/PathwayAssessor/tree/master/pathway_assessor).\n\n```\nimport pathway_assessor as pa\n\npa.all()\npa.harmonic()\npa.geometric()\npa.min_p_val()\n```\n\n\n## References \n1. Barbie, D.A. , et al. \u201cSystematic RNA interference reveals\u2026\u201d, Nature. 2009 Nov 5;462(7269):108-12.\n2. Abril-Rodrigues, G., Ribas A., \u201cSnapShot: Immune Checkpoint Inhibitors\u201d, Cancer Cell 31, June 12, 2017.\n3. Aran, D., Hu Z., Butte, A. \u201cxCell: digitally portraying the tissue\u2026\u201d, Genome Biology. (2017) 18:220. \n\n### Contributions\n\nIf you find small bugs, larger issues, or have suggestions, please email the maintainer at .\nContributions (via pull requests or otherwise) are welcome.\n\n\n",
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