Predict Cell Types

The Predict Cell Types tool uses a Cell Type Classifier (Image cell_type_classifier_16_n_p) to automatically assign cell types to the cells in the Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p) provided as input.

It can be found in the Toolbox here:

        Gene Expression (Image sc_gene_expression_folder_open_16_n_p) | Cell Type Classification (Image sc_cell_annotation_folder_open_16_n_p) | Predict Cell Types (Image predict_celltypes_16_n_p)

The following options can be adjusted (figure 6.2):

Image predict_cell_types
Figure 6.2: The options in the dialog of the Predict Cell Types tool. A Cell Type Classifier for human data downloaded from the Reference Data Manager has been selected.

The tool outputs:

Using the outputs, the cells can be colored in a Dimensionality Reduction Plot (see Dimensionality reduction) by the predicted cell type (using the Cell Clusters) or the probability of having a specific cell type (using the Cell Annotations). Guided by the probabilities and other information, such as the clusters produced by the Cluster Single Cell Data tool (see Cluster Single Cell Data), the predicted cell types can be manually refined in the Dimensionality Reduction Plot (see Manual Annotation).

For details on how cell types are predicted, see SVMs for cell type classification.