Classification
There are different methods to automatically classify cell type based on biomarkers. There are two methods available in Connected Multiomics
SCtype
Garnett
Cell Typing with ScType
ScType allows automated cell-type identification based on scRNA-seq data along with a comprehensive cell marker database as background information.
Click the data node containing the non-normalized count matrix
Click on Classification > Single cell type in the toolbox
Select the marker database from the drop-down menu, the original full ScType database is provided by default
Select categorical attributes to Categorize by (e.g. graph-based clusters)
Optionally Filter tissue types
Select the SC Type algorithm to use
Click Configure to access and change any Advanced options
Click Finish to run
A new scType classification task node will be produced. When complete, double-click the Single cell type node to open the results of the cell-type identification. For each cell, the tissue, sctype result, and typescore are reported.
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