abagen
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rmarkello
A toolbox for working with Allen Human Brain Atlas microarray expression data
## The issue [Burt et al., 2018](https://www.nature.com/articles/s41593-018-0195-0) performed their analyses using pre-determined groups of genes (i.e., "brain-specific," "neuron- and oligodendrocyte-specific," etc.). It would be nice to incorporate these "standard" sets...
Thanks to @yingqiuz, `abagen` can now query the Allen Brain database for mouse *in situ* hybridization data! :tada: Unfortunately, this is documented exactly nowhere outside of the codebase. This should...
Hi， A couple days ago, I ran the following code and it was working, but now it's reporting an error，and I don't know how to fix this: `import nibabel as...
Hi, I noticed that my generated expression file contains fewer entries than the atlas I used, which I dont understand. More specifically I am using an atlas with 170 regions...
I have identified a potential bug within the check_surface function of images.py, specifically between lines 297-301. The code segment is designed to prevent the overlapping of labels across hemispheres and...
Would be very nice if `abagen.get_expression_data` would also return a list-like object of gene-groups (e.g. dopaminergic, noradrenergic, cholinergic, etc) that would allow for a quicker subsection of the returned dataframe...
Hello, I am new to abagen and I still have couple questions after going through the user-guide. What we would like to do is to access the gene expression in...
[https://github.com/rmarkello/abagen/blob/6f5542522247b9a7fb00ded198c34f4dc25957f3/abagen/samples_.py#L220C1-L224C46](url) Line 220-224 in samples_.py ``` annot = annotation.assign(hemisphere=hemisphere, structure=structure) \ .query('(hemisphere == "L" & mni_x < 0) ' '| (hemisphere == "R" & mni_x > 0) ' '| (hemisphere...
hello everyone , I want to obtain the samples*gene matrix after some necessary processing steps but before gene expression values in samples are merged (eg. mean) in different brain regions....
Hi, recently I was trying to use abagen to analyze the AHBA data with Brainnetome atlas but found the returned variable `expression, coords` of `abagen.get_samples_in_mask` dropped the true samples lying...
