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Replace cell classifier #29

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azedinez opened this issue Mar 23, 2023 · 0 comments
Open

Replace cell classifier #29

azedinez opened this issue Mar 23, 2023 · 0 comments
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enhancement Improvement for existing functionality

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@azedinez
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Is your feature request related to a problem? Please describe

It looks like the current cell classifier is limited to brain cells only.

Describe the solution you'd like

It would be great to use a cell classifier for a broader range of tissue types. It seems that the Garnett tool seem pretty adequate for that task https://cole-trapnell-lab.github.io/garnett/classifiers/ - and new classifiers might be created for the tissue types that are not currently covered, and then used as part of the tool.

Describe alternatives you've considered

scCatch was also considered as it contains a very broad range of cell types. However, on closer inspections, some cell signatures are derived from only one or two genes and some of the cell types don't match their tissue of origin. https://github.com/ZJUFanLab/scCATCH

@azedinez azedinez added the enhancement Improvement for existing functionality label Mar 23, 2023
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