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This repository was archived by the owner on Jun 13, 2024. It is now read-only.
This repository was archived by the owner on Jun 13, 2024. It is now read-only.

Replace cell classifier #29

Description

@azedinez

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

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