Classify cell type
Garnett[1] automated cell type classification method should be invoked from a non-normalized raw count matrix data node. It use the specified classifier to generate cell type annotation on the input data
Select a raw count data node, choose Classification > Classify cell type task on the pop-up menu
If using the Managed classifiers tool for the first time, you will be asked to create a new classifier file. Users may select either the Download Garnett classifier that matches the species and tissue type with their dataset or the Import Garnett classifier that is trained previously.
Next, click the Create button to create the classifier file. Once the correct classifier file has been created, select Finish to start running the task.
If you would like to classify cell type with the classifier obtained from the same analysis, choose Project classifiers, and click on ‘Select data node’ to choose the classifier in the analysis. Details on how to train a classifier can be found here. Then click the Finish button.
The output data node named Classify result, it contains the cell type annotation attributes, "cell_type" is the cell type assignments directly from Garnett model. While "cluster_ext_type" is the cell type that's determined by expanding cell type assignments to nearby cells using Louvain clustering. Downstream analysis tasks such as normalization and PCA can be performed on the Classify result data node.
References
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