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        "author": "Florian Finkernagel",
        "author_email": "finkernagel@imt.uni-marburg.de",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: Implementation :: CPython",
            "Programming Language :: Python :: Implementation :: PyPy"
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        "description": "# marburg_biobank\n## Introduction\n\nThe marburg_biobank python module offers a high level interface to the data sets\nstored in the [Ovarian Cancer Effusion Biobank and Database])(https://www.ovara.net/biobank).\n\nThe basic usage is as follows:\n```python\n\nimport marburg_biobank\ndb = marburg_biobank.OvcaBiobank(\"marburg_ovca_revision_15.zip\") #  you need to download that file from your biobank.\nprint(db.list_datasets())\ndf_wide = db.get_wide('transcriptomics/rnaseq')  # to retrieve the data in a one sample per column / one row per measured variable format\ndf_tall = db.get_dataset('transcriptomics/rnaseq') # to retrieve the data in one row per data point format\n```\n\n\n## Data formats available\n\n### wide\nUsing ```db.get_wide(dataset)```:\n\nA pandas DataFrame that looks like this\n\n| Index | Patient12, TAM | Patient12, TU | PatientX, Compartment\n| ----- | --------------- | -------------- | ------------------------\n| **VariableA, unitA** | 23.23 | 112.2 | nan |\n| **VariableB, unitB** | 3.23 | 12.2 | 12.7 |\n\n\nCaveats: If a dataset has only one compartment, the compartment information is ommited by get_wide(), unless .get_wide(standardized=True) is used.\nThe same applies for the unit in the index.\nIf there is a 'name' column in dataset, it get's added to the index, regardless of the value of standardized.\n\n### tall\n\nUsing: ```db.get_dataset(dataset)```):\n\nA pandas DataFrame that looks like this\n\n|variable | unit | patient | compartment | value | optional columns...\n| ------- | ---- | ------- | ----------- | ----- | ----- |\n| variableA | unitA | Patient12 | TAM | 23.23| |\n| variableA | unitA | Patient12 | TU | 112.2| |\n| variableB | unitB | Patient13 | TAM | 3.23| |\n| variableB | unitB | Patient13 | TU | 12.2| |\n\nThis is the internal storage format.\n\n\n## compartments\n Compartments are an abstraction on top of 'cells' and 'bio-liquid'. Examples are Tumor associated macrophages (TAMs), Tumor cells (TU), ascites, blood...\n ```db.get_compartments()``` provides a list\n\n## Datasets\n\nDatasets are organized three levels deep. The first one defines the whether\nyou're looking t ex-vivo (=primary) data or in-vitro experiments (=secondary) \nor literature data (=tertiary).\nThe second level defines *omics being measured (transcriptomics, proteomics, ... or 'clinical'), while\nthe third levels defines the actual method (RNaseq, FACS,...)\n\nSurvival data is in primary/clinical/survival. \n\nPlease remember: if using [https://pypi.python.org/pypi/lifelines](lifelines), censored and event are negations of each other.\n\n## Excluded patients:\n\nExclusion can either be on a patient, or a patient+compartment level.\nIn addition, there is per dataset exclusion and global exclusion.\n\nExclusion is by default applied to db.get_wide(), but not to db.get_dataset(),\nyou can change the default by passing apply_exclusion=True|False.\n\nExclusion information can be retrieved by db.get_excluded_patients(dataset),\nwhich return a set of patients (or patient+compartment tuples),\nor db.get_exclusion_reasons(), which lists why the exclusion happend.",
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        "license": "MIT",
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        "name": "marburg-biobank",
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        "project_url": "https://pypi.org/project/marburg-biobank/",
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        "release_url": "https://pypi.org/project/marburg-biobank/0.124/",
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        "summary": "Interface code to interact with data from the Ovara.net biobank.",
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