Metadata-Version: 2.1
Name: abagen
Version: 0.0.1
Summary: A toolbox for working with the Allen Brain Atlas human genetic data
Home-page: https://github.com/rmarkello/abagen
Maintainer: Ross Markello
Maintainer-email: rossmarkello@gmail.com
License: BSD-3
Download-URL: http://github.com/rmarkello/abagen/archive/0.0.1.tar.gz
Description: abagen: A toolbox for the Allen Brain Atlas genetics data
        =========================================================
        
        This package provides a Python interface for working with the `Allen Human
        Brain Atlas <http://human.brain-map.org/>`_ (AHBA) microarray expression data.
        
        .. image:: https://travis-ci.org/rmarkello/abagen.svg?branch=master
           :target: https://travis-ci.org/rmarkello/abagen
        .. image:: https://codecov.io/gh/rmarkello/abagen/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/rmarkello/abagen
        .. image:: https://readthedocs.org/projects/abagen/badge/?version=latest
           :target: http://abagen.readthedocs.io/en/latest
        .. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
           :target: https://opensource.org/licenses/BSD-3-Clause
        
        .. _overview:
        
        Overview
        --------
        
        In 2013, the Allen Institute for Brain Science released the Allen Human Brain
        Atlas, `a dataset <http://human.brain-map.org/>`_ containing microarray
        expression data collected from six human brains. This dataset has offered an
        unprecedented opportunity to examine the genetic underpinnings of the human
        brain, and has already yielded novel insight into e.g., `adolescent brain
        development <http://www.pnas.org/content/113/32/9105.long>`_ and `functional
        brain organization <http://science.sciencemag.org/content/348/6240/1241.long>`_.
        
        However, in order to be effectively used in most analyses, the AHBA microarray
        expression data often needs to be (1) collapsed into regions of interest (e.g.,
        parcels or networks), and (2) combined across donors. While this may
        potentially seem trivial, there are numerous analytic choices in these steps
        that can dramatically influence the resulting data and any downstream analyses.
        Indeed, Arnatkevičiūte et al., 2018 ([1]_) provided a thorough treatment of
        this in a `recent manuscript <https://www.biorxiv.org/content/early/2018/07/30/
        380089>`_, demonstrating how the techniques and code used to prepare the raw
        AHBA data have varied widely across published reports.
        
        The current Python package, ``abagen``, aims to provide a reproducible pipeline
        for processing and preparing the AHBA microarray expression data for analysis.
        If you'd like more information about the package, including how to install it
        and some example instructions on its use, check out our `documentation <https:
        //abagen.readthedocs.io>`_!
        
        .. _development:
        
        Development and getting involved
        --------------------------------
        
        This package has been largely developed in the spare time of a single graduate
        student (`@rmarkello <https://github.com/rmarkello>`_) with help from some
        incredible `contributors <https://github.com/rmarkello/abagen/graphs/
        contributors>`_. While it would be |sparkles| amazing |sparkles| if anyone else
        finds it helpful, given the limited time constraints of graduate school, the
        current package is not currently accepting requests for new features.
        
        However, if you're interested in getting involved in the project, we're
        thrilled to welcome new contributors! You shouldstart by reading our
        `contributing guidelines <https://github.com/rmarkello/abagen/blob/master/
        CONTRIBUTING.md>`_ and `code of conduct <https://github.com/rmarkello/abagen/
        blob/master/CODE_OF_CONDUCT.md>`_. Once you're done with that, take a look at
        our `issues <https://github.com/rmarkello/abagen/issues>`_ to see if there's
        anything you might like to work on. Alternatively, if you've found a bug, are
        experiencing a problem, or have a question, create a new issue with some
        information about it!
        
        .. _acknowledgments:
        
        Acknowledgments
        ---------------
        
        While this package was initially created in early 2018, many of the current
        functions in the project were inspired by the workflow laid out in
        Arnatkevičiūte et al., 2018. As such, if you use this code it would be good
        to (1) provide a link back to the ``abagen`` repository with the version of the
        code used, and (2) cite their paper:
        
        .. [1] Arnatkeviciute, A., Fulcher, B. D., & Fornito, A. (2018). A practical
           guide to linking brain-wide gene expression and neuroimaging data. bioRxiv,
           380089.
        
        .. _licensing:
        
        License Information
        -------------------
        
        This codebase is licensed under the 3-clause BSD license. The full license can
        be found in the `LICENSE <https://github.com/rmarkello/abagen/blob/master/
        LICENSE>`_ file in the ``abagen`` distribution.
        
        All trademarks referenced herein are property of their respective holders.
        
        .. |sparkles| replace:: ✨
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/x-rst
Provides-Extra: all
Provides-Extra: io
Provides-Extra: doc
Provides-Extra: tests
