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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