scaled or arcsinh-transformed expression for annotation?

Thank you for developing this excellent tool.

In the manuscript, it suggested to use the heatmap from Figure 6 to annotate clusters, but we have a question regarding the use of scaled expression values (0-1). Since this scaling can artificially inflate low-expression markers, would using arcsinh-transformed values be a more appropriate method for cluster annotation?

Start with the manuscript’s discussion of Figure 6 and the heatmap guidance for cluster annotation. Compare the stated use of scaled expression values with the question about arcsinh-transformed values; done would be a resolved, documented recommendation, but the issue names no implementation file or test.

Written by the indexing model from the issue text.