abagen
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rmarkello
A toolbox for working with Allen Human Brain Atlas microarray expression data
- [ ] Update docs about using and the risk of using custom parcellation, including code samples and links to useful functions in neuromaps and netneurotools. - [ ] Update...
Dear all, I want to identify differential expressed genes (DEGs) between ROIs (for example, PFC versus the rest of brain) using limma R package, after parcellation through the `abagen.get_expression_data` function....
Dear Abagen Team, Thank you for creating this wonderful resource. It must have been a huge amount of work I'm trying to download the microarray data using files = abagen.fetch_microarray(donors='all')...
Dear all This is my first time using python and abagen. I am replicating the tutorial by jupyter. All works well until section 3.1. When I run expression = abagen.get_expression_data(atlas['image'],...
There is a error while add parameter `--ibf_threshold 0.5` in command line ```bash Traceback (most recent call last): File "/usr/local/bin/abagen", line 8, in sys.exit(main()) File "/usr/local/lib/python3.10/dist-packages/abagen/cli/run.py", line 365, in main...
Could you please introduce how to make Destrieux atlas（label.gii）file and corresponding surf file ? Thank you very much!
I am trying to obtain sample-level expression data for each of 8 components (~parcels) from a data-driven cortical decomposition performed in CIVET space. I have both a LH/RH binary mask...
the test on `tests/mouse/test_gene.py` could fail when retrieving the GENE data with a list contains 17943 The original test fails on the 36th run with the current random seed. the...
Hi there, Great package thanks for sharing! I am trying to use the relabel_gifti function however I keep running into a small issue. For context: I am trying to get...
Hi again, I noticed that certain sub-cortex structures are not included in the version of the DK atlas provided with `abagen`, like the cerebellum, ventricles, and other. Would it be...
