abagen
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rmarkello
A toolbox for working with Allen Human Brain Atlas microarray expression data
I "published" an improved MNI-space registration based on Chris' original work: https://github.com/gdevenyi/AllenHumanGeneMNI Mostly the registrations tried harder, and I managed to fix the subject with the terrible cerebellum.
## The issue In addition to the MNI coordinates of each sample, the Allen Institute provides a detailed ontology of the brain structure each sample was ostensibly taken from in...
In the section of Donor normalization, with the Batch correction command line: abagen.get_expression_data(atlas['image'], donor_norm='batch') I got the following error message: raise ValueError('Cannot perform batch correction with one batch.') ValueError: Cannot...
## The issue `abagen` currently does a lot of leg work for going from the microarray expression data obtained via the AHBA to parcellated expression data. But, after that, things...
## The issue As Arnatkevičiūte et al., 2019 pointed out in their manuscript, some of the probes in the AHBA data were incorrectly (or not) annotated to genes. Since the...
## The issue As of #105 we have some vastly improved contributing guidelines! To help smooth out the contribution process even more it would be great to include [issue and...
## The issue The `abagen.mouse` module provides some functionality for making Pythonic queries to the [Allen API](http://help.brain-map.org/display/api/Allen+Brain+Atlas+API). For example, to get gene expression data for Prodynorphin from the anterior cingulate...
## The issue In the current workflow for `abagen.get_expression_data()` there are a few calls to the `probes.filter_probes()` and `probes.collapse_probes()` functions, both of which use microarray expression data from donors to...
## The issue There was a really nice paper last year by [Gryglewski et al., 2018](https://www.ncbi.nlm.nih.gov/pubmed/29723639) that used some variogram modelling to generate "smooth" microarray expression maps for all the...
Currently `abagen.get_expression_data()` takes a really long time (this should also probably be addressed...) and provides exactly zero information about its progress during that period. It would be _fantastic_ to add...