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Mirror `abagen.mouse` functionality for human API

Open rmarkello opened this issue 5 years ago • 0 comments

The issue

The abagen.mouse module provides some functionality for making Pythonic queries to the Allen API. For example, to get gene expression data for Prodynorphin from the anterior cingulate of the mouse, you would call:

>>> from abagen import mouse
>>> mouse.get_unionization_from_gene(name='prodynorphin', 
...                                  structures='Anterior cingulate area')
                      expression_density
gene_id structure_id                    
18376   31                      0.017199

Though the mouse module hasn't received much attention since #32, it might be nice to have a similar module for querying information from the human API.

Proposed solution

I'm thinking that having an abagen.api module could hold all this for the human data and would be designed similar to the abagen.mouse module. An example function could include:

>>> from abagen import api
>>> api.get_expression_from_gene(name='prodynorphin', donors='9861',
...                              structures='cingulate gyrus')

This is quite an open-ended enhancement so happy to workshop things a bit!

rmarkello avatar Sep 13 '19 15:09 rmarkello