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abagen: A toolbox for the Allen Brain Atlas genetics data

This package provides a Python interface for fetching and working with the Allen Human Brain Atlas (AHBA) microarray expression data.

🚨 🚨 WARNING: This package is in alpha and should be considered unstable! Things are liable to be changed with limited consideration for backwards compatibility, so please use carefully. 🚨 🚨

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Overview

In 2013, the Allen Institute for Brain Science released the Allen Human Brain Atlas, a dataset containing microarray expression data collected from six human brains (Hawrylycz et al., 2012) . 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 and functional brain organization.

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 a number of analytic choices in these steps that can dramatically influence the resulting data and any downstream analyses. Arnatkevičiūte et al., 2019 provided a thorough treatment of this in a recent `manuscript, 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 reproducible workflows for processing and preparing the AHBA microarray expression data for analysis.

Installation requirements

Currently, abagen works with Python 3.5+ and requires a few dependencies:

  • nibabel
  • numpy (>=1.14.0)
  • pandas, and
  • scipy

There are some additional (optional) dependencies you can install to speed up some functions:

  • fastparquet, and
  • python-snappy

These latter packages are primarily used to facilitate loading the (rather large!) microarray expression dataframes provided by the Allen Institute,

For detailed information on how to install abagen, including these dependencies, refer to our installation instructions.

Quickstart

At it's core, using abagen is as simple as:

>>> import abagen
>>> expression = abagen.get_expression_data('myatlas.nii.gz')

where 'myatlas.nii.gz' points to a Nifti file that defines a brain parcellation in MNI space.

This function can also be called from the command line with:

$ abagen --output-file expression.csv myatlas.nii.gz

For more detailed instructions on how to use abagen please refer to our user guide!

Development and getting involved

If you've found a bug, are experiencing a problem, or have a question about using the package, please head on over to our GitHub issues and make a new issue with some information about it! Someone will try and get back to you as quickly as possible, though please note that the primary developer for abagen (@rmarkello) is a graduate student so responses make take some time!

If you're interested in getting involved in the project: welcome ✨! We're thrilled to welcome new contributors. You should start by reading our code of conduct; all activity on abagen should adhere to the CoC. After that, take a look at our contributing guidelines so you're familiar with the processes we (generally) try to follow when making changes to the repository! Once you're ready to jump in head on over to our issues to see if there's anything you might like to work on.

Citing abagen

For up-to-date instructions on how to cite abagen please refer to our documentation.

License Information

This codebase is licensed under the 3-clause BSD license. The full license can be found in the LICENSE file in the abagen distribution.

Reannotated gene information located at abagen/data/reannotated.csv.gz is taken from Arnatkevičiūte et al., 2018 and is separately licensed under the CC BY 4.0; these data can also be found on figshare.

Corrected MNI coordinates used to match AHBA tissues samples to MNI space located at abagen/data/corrected_mni_coordinates.csv are taken from the alleninf package, provided under the 3-clause BSD license.

All microarray expression data is copyrighted under non-commercial reuse policies by the Allen Institute for Brain Science (© 2010 Allen Institute for Brain Science. Allen Human Brain Atlas. Available from: Allen Human Brain Atlas).

All trademarks referenced herein are property of their respective holders.