AllenInstitute / AllenInstitute/AllenInstituteTaxonomy
Code Updates to scrattch_taxonomy_py
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@inkarkapen is already working on this.
Since Sep 16, 2026.
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Description
- Add validation check to make sure uns['cluster_info'] has all the files from the uns['herarchy'] and matches and limits to only names from those herarchy column values in obs.
- AiT will move to also allow .zarr format. Operations we need to perform on large data are more efficient in zarr format.
- Explore if any compression methods are needed like gzip etc or just zarr.
- Make it easy to cell (obs) subsetting. Whether that is to use CSR matrix or any other ideas.
- AiT will store only a count matrix as unsigned int32. We won't store both count and logCPM anymore. We will store pre-computed normalizing factors to on-the-fly logCPM.
- Make tests that use Tasic et al. 2016 dataset and run the code to build the AiT.
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