{ "info": { "author": "Ross Markello", "author_email": "rossmarkello@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6" ], "description": ".. Following contents should be from LONG_DESCRIPTION in abagen/info.py\n\n\nabagen: A toolbox for the Allen Brain Atlas genetics data\n=========================================================\n\nThis package provides a Python interface for fetching and working with the\n`Allen Human Brain Atlas`_ (AHBA) microarray expression data.\n\n|warning| |warning| **WARNING**: This package is in alpha and should be\nconsidered unstable! Things are liable to be changed with limited consideration\nfor backwards compatibility, so please use carefully. |warning| |warning|\n\n.. image:: https://travis-ci.org/rmarkello/abagen.svg?branch=master\n :target: https://travis-ci.org/rmarkello/abagen\n.. image:: https://codecov.io/gh/rmarkello/abagen/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/rmarkello/abagen\n.. image:: https://readthedocs.org/projects/abagen/badge/?version=latest\n :target: https://abagen.readthedocs.io/en/stable\n.. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg\n :target: https://opensource.org/licenses/BSD-3-Clause\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3451463.svg\n :target: https://doi.org/10.5281/zenodo.3451463\n\n.. _readme_overview:\n\nOverview\n--------\n\nIn 2013, the Allen Institute for Brain Science released the `Allen Human Brain\nAtlas`_, a dataset containing microarray expression data collected from six\nhuman brains (Hawrylycz et al., 2012) . This dataset has offered an\nunprecedented opportunity to examine the genetic underpinnings of the human\nbrain, and has already yielded novel insight into e.g., `adolescent brain\ndevelopment `__ and `functional\nbrain organization `__.\n\nHowever, in order to be effectively used in most analyses, the AHBA microarray\nexpression data often needs to be (1) collapsed into regions of interest (e.g.,\nparcels or networks), and (2) combined across donors. While this may\npotentially seem trivial, there are a number of analytic choices in these steps\nthat can dramatically influence the resulting data and any downstream analyses.\nArnatkevi\u010di\u016bte et al., 2019 provided a thorough treatment of this in a `recent\n`manuscript `__, demonstrating how the techniques and code used to\nprepare the raw AHBA data have varied widely across published reports.\n\nThe current Python package, ``abagen``, aims to provide reproducible workflows\nfor processing and preparing the AHBA microarray expression data for analysis.\n\n.. _readme_requirements:\n\nInstallation requirements\n-------------------------\nCurrently, ``abagen`` works with Python 3.5+ and requires a few dependencies:\n\n - nibabel\n - numpy (>=1.14.0)\n - pandas, and\n - scipy\n\nThere are some additional (optional) dependencies you can install to speed up\nsome functions:\n\n - fastparquet, and\n - python-snappy\n\nThese latter packages are primarily used to facilitate loading the (rather\nlarge!) microarray expression dataframes provided by the Allen Institute,\n\nFor detailed information on how to install ``abagen``, including these\ndependencies, refer to our `installation instructions`_.\n\n.. _readme_usage:\n\nQuickstart\n----------\n\nAt it's core, using ``abagen`` is as simple as:\n\n.. code-block:: python\n\n >>> import abagen\n >>> expression = abagen.get_expression_data('myatlas.nii.gz')\n\nwhere ``'myatlas.nii.gz'`` points to a Nifti file that defines a brain\nparcellation in MNI space.\n\nThis function can also be called from the command line with:\n\n.. code-block:: bash\n\n $ abagen --output-file expression.csv myatlas.nii.gz\n\nFor more detailed instructions on how to use ``abagen`` please refer to our\n`user guide`_!\n\n.. _readme_development:\n\nDevelopment and getting involved\n--------------------------------\n\nIf you've found a bug, are experiencing a problem, or have a question about\nusing the package, please head on over to our `GitHub issues`_ and make a new\nissue with some information about it! Someone will try and get back to you\nas quickly as possible, though please note that the primary developer for\n``abagen`` (@rmarkello) is a graduate student so responses make take some time!\n\nIf you're interested in getting involved in the project: welcome |sparkles|!\nWe're thrilled to welcome new contributors. You should start by reading our\n`code of conduct`_; all activity on ``abagen`` should adhere to the CoC. After\nthat, take a look at our `contributing guidelines`_ so you're familiar with the\nprocesses we (generally) try to follow when making changes to the repository!\nOnce you're ready to jump in head on over to our issues to see if there's\nanything you might like to work on.\n\n.. _readme_acknowledgments:\n\nCiting ``abagen``\n-----------------\n\nFor up-to-date instructions on how to cite abagen please refer to our\n`documentation `_.\n\n.. _readme_licensing:\n\nLicense Information\n-------------------\n\nThis codebase is licensed under the `3-clause BSD license`_. The full license\ncan be found in the `LICENSE`_ file in the ``abagen`` distribution.\n\nReannotated gene information located at ``abagen/data/reannotated.csv.gz`` is\ntaken from Arnatkevi\u010di\u016bte et al., 2018 and is separately licensed under the `CC\nBY 4.0`_; these data can also be found on `figshare `__.\n\nCorrected MNI coordinates used to match AHBA tissues samples to MNI space\nlocated at ``abagen/data/corrected_mni_coordinates.csv`` are taken from the\n`alleninf package`_, provided under the `3-clause BSD license`_.\n\nAll microarray expression data is copyrighted under `non-commercial reuse\npolicies`_ by the Allen Institute for Brain Science (\u00a9 2010 Allen Institute for\nBrain Science. Allen Human Brain Atlas. Available from: `Allen Human Brain\nAtlas`_).\n\nAll trademarks referenced herein are property of their respective holders.\n\n.. |sparkles| replace:: \u2728\n.. |warning| replace:: \ud83d\udea8\n.. _3-clause BSD license: https://opensource.org/licenses/BSD-3-Clause\n.. _Allen Human Brain Atlas: https://human.brain-map.org/\n.. _alleninf package: https://github.com/chrisfilo/alleninf\n.. _CC BY 4.0: https://creativecommons.org/licenses/by/4.0/legalcode\n.. _code of conduct: https://github.com/rmarkello/abagen/blob/master/CODE_OF_CONDUCT.md\n.. _contributing guidelines: https://github.com/rmarkello/abagen/blob/master/CONTRIBUTING.md\n.. _contributors: https://github.com/rmarkello/abagen/graphs/contributors\n.. _user guide: https://abagen.readthedocs.io/en/stable/usage.html\n.. _GitHub issues: https://github.com/rmarkello/abagen/issues\n.. _installation instructions: https://abagen.readthedocs.io/en/stable/installation.html\n.. _LICENSE: https://github.com/rmarkello/abagen/blob/master/LICENSE\n.. _non-commercial reuse policies: https://alleninstitute.org/legal/terms-use/\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "https://github.com/rmarkello/abagen", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/rmarkello/abagen", "keywords": "", "license": "BSD-3", "maintainer": "", "maintainer_email": "", "name": "abagen", "package_url": "https://pypi.org/project/abagen/", "platform": "OS Independent", "project_url": "https://pypi.org/project/abagen/", "project_urls": { "Download": "https://github.com/rmarkello/abagen", "Homepage": "https://github.com/rmarkello/abagen" }, "release_url": "https://pypi.org/project/abagen/0.0.2/", "requires_dist": [ "nibabel", "numpy (>=1.14)", "pandas", "scipy", "sphinx (>=2.0); 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