Compare Cell Clonotypes

Compare Cell Clonotypes contrasts properties, such as diversity and similarity, of the immune repertoires identified for groups of cells, as determined by the sample or, when available, through Cell Clusters (Image cell_clusters_16_n_p) or Cell Annotations (Image cell_annotations_16_n_p).

The Compare Cell Clonotypes tool can be found in the Toolbox here:

        Immune Repertoire (Image sc_immune_rept_folder_open_16_n_p) | Compare Cell Clonotypes (Image sc_immune_rept_compare_16_n_p)

The tool takes a TCR Cell Clonotypes (Image cell_tcr_clonotypes_16_n_p) or BCR Cell Clonotypes (Image cell_bcr_clonotypes_16_n_p) element as input. If the clonotypes to be compared are found in different elements, these can be combined using the Combine Cell Clonotypes tool, see Combine Cell Clonotypes for details.

The following options can be adjusted (figure 10.5):

Image compare_repertoires_wizard
Figure 10.5: The default options in the dialog of the Compare Cell Clonotypes tool. Note that "Group by" needs to contain at least one value before proceeding. This can always be set to "Sample".