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IGS / gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
https://umgear.org
GNU Affero General Public License v3.0
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Test upgrading scanpy/anndata #670

Open adkinsrs opened 1 month ago

adkinsrs commented 1 month ago

When we redesign the single-cell workbench page, I think it would be a great time to update the scanpy and anndata packages. I made a branch "scanpy-1.9.8-upgrade" where I will install the latest versions of several packages and test them out. I already have been doing a bit of work on this, and found a couple of small bugs that have been cleaned up. Another nice perk is some of our own code can be condensed or removed due to new options from scanpy.

Scanpy -> 1.9.8 Anndata -> 0.10.6 pandas -> 2.2.1 h5py -> 3.10.0 (and other things)

jorvis commented 1 month ago

This will be very nice to have done!

adkinsrs commented 1 month ago

Testing sc workbench is done. Single gene curator is done though I did not exhaust every single possible option. Expression and projection pages also complete (generally these plots also overlap with testing the curators)

todo- compare tool and multigene curator.