Package: abagen
This package provides a Python interface for fetching and working with theAllen Human Brain Atlas(AHBA) microarray expression data.OverviewIn 2013, the Allen Institute for Brain Science released theAllen 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
developmentandfunctional
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 arecent
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 requirementsCurrently,abagenworks with Python 3.6+ and requires a few dependencies:nibabelnumpy (>=1.14.0)pandas (>=0.25.0), andscipyThere are some additional (optional) dependencies you can install to speed up
some functions:fastparquet, andpython-snappyThese 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 installabagen, including these
dependencies, refer to ourinstallation instructions.QuickstartAt it’s core, usingabagenis as simple as:>>>importabagen>>>expression=abagen.get_expression_data('myatlas.nii.gz')where'myatlas.nii.gz'points to a brain parcellation file.This function can also be called from the command line with:$abagen--output-fileexpression.csvmyatlas.nii.gzFor more detailed instructions on how to useabagenplease refer to ouruser guide!Development and getting involvedIf you’ve found a bug, are experiencing a problem, or have a question about
using the package, please head on over to ourGitHub issuesand 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 forabagen(@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 ourcode of conduct; all activity onabagenshould adhere to the CoC. After
that, take a look at ourcontributing guidelinesso 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.CitingabagenFor up-to-date instructions on how to cite abagen please refer to ourdocumentation.License InformationThis codebase is licensed under the3-clause BSD license. The full license
can be found in theLICENSEfile in theabagendistribution.Reannotated gene information located atabagen/data/reannotated.csv.gzand
individualized donor parcellations for the Desikan-Killiany atlas located atabagen/data/native_dkare taken from Arnatkevičiūte et al., 2018 and are
separately licensed under theCC BY 4.0; these data can also be found onfigshare.Corrected MNI coordinates used to match AHBA tissues samples to MNI space
located atabagen/data/corrected_mni_coordinates.csvare taken from thealleninf package, provided under the3-clause BSD license.All microarray expression data is copyrighted undernon-commercial reuse
policiesby 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.