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        "author": "Keiron O'Shea",
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        "classifiers": [
            "Development Status :: 4 - Beta",
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            "Programming Language :: Python :: 3.6",
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        "description": "# pyMEAN: Metabolomic Enrichment ANalysis in Python\n\nThe pyMEAN package is designed to facilitate semi-automated enrichment analysis for metabolomic experiments.\n\n## Installation\n\npyMEAN requires Python 3+ and is unfortunately not compatible with Python 2. If you are still using Python 2, a clever workaround is to install Python 3 and use that instead.\n\nThe easiest way of installing pyMEAN is using pip:\n\n```\npip install pymean\n```\n\nAlternatively, you can use git and pip in unison to get the development branch:\n\n```\npip install https://github.com/KeironO/pyMEAN\n```\n\n## Usage\n\nHere's a starting template to get you started:\n\n```python\n# Import pyMEAN module into Python.\nfrom pymean import EnrichmentAnalysis\n\n# A compound list of inchikeys.\ncompound_list = [\n    \"WDJHALXBUFZDSR-UHFFFAOYSA-N\", # acetoacetic acid\n    \"UCMIRNVEIXFBKS-UHFFFAOYSA-N\", # beta-alanine\n    \"CVSVTCORWBXHQV-UHFFFAOYSA-N\", # creatine\n    \"FFDGPVCHZBVARC-UHFFFAOYSA-N\", # dimethylglycine\n    \"VZCYOOQTPOCHFL-OWOJBTEDSA-N\", # fumaric acid\n    \"DHMQDGOQFOQNFH-UHFFFAOYSA-N\", # glycine\n    \"FFFHZYDWPBMWHY-UHFFFAOYSA-N\", # l-homocysteine\n    \"XUJNEKJLAYXESH-REOHCLBHSA-N\", # l-cysteine\n    \"COLNVLDHVKWLRT-QMMMGPOBSA-N\", # l-phenylalanine\n    \"BTNMPGBKDVTSJY-UHFFFAOYSA-N\" # phenylpyruvic acid\n]\n\n\n# Create an EnrichmentAnalysis object for the analysis of hsa\nea = EnrichmentAnalysis(compound_list, organism=\"hsa\")\n\n# Run the analysis\nea.run_analysis(pvalue_cutoff=0.05)\n\n# Obtain results (in the format of a pandas dataframe)\nresuklts = ea.results\n\n```\n\nIf you'd like to plot out your results, take inspiration from the following method:\n\n```python\ndef plot_enrichment_analysis_results(results: pd.DataFrame, adj_method:str):\n    fold_enrichment = np.abs(np.log(results[\"%s adj. p-value\" % (adj_method)]))\n    plt.figure()\n    plt.title(\"Metabolite Sets Enrichment Overview\")\n    plt.barh(results[\"Pathway Name\"], fold_enrichment, height=0.5)\n    plt.xlabel(\"Fold Enrichment\")\n\n    plt.yticks(fontsize=6)\n    plt.tight_layout()\n\n    plt.show()\n\nplot_enrichment_analysis_results(results, \"fdr_bh\")\n\n```\n\nWhich will return the following chart:\n\n![Plot of results](https://github.com/AberystwythSystemsBiology/pyMEAN/raw/master/example.png)\n\n## License\n\nCode released under the [GPLv3](https://github.com/AberystwythSystemsBiology/pyMEAN/blob/master/LICENSE).",
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        "keywords": "metabolomics,enrichment analysis,omics",
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        "name": "pymean",
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