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. 2024 Feb 26;25:56. doi: 10.1186/s13059-024-03183-0

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 4 — Comparison of methods based on expert-annotated marker genes. a Recall of methods when selecting marker genes in the Lawlor dataset using a set of expert-annotated marker genes as the ground truth. The marker genes used to annotate the clustering in the original publication describing the Lawlor dataset were used as the set of expert-annotated marker genes. The top gene was selected from the output of each method. b As in (a) but for the pbmc3k dataset, using the (at most) top 10 marker genes from each method and taking the set of expert-annotated marker genes to be those used in the Seurat package’s “Guided Clustering Tutorial.” c The number of clusters that are successfully annotated using the selected marker genes in the Lawlor datasets (other details as in a). A specific cluster is defined as successfully annotated if the selected marker genes include all the expert-annotated marker genes for that cluster. d The same success of annotation analysis as in (c) but for the pbmc3k dataset, with the details of the expert-annotated marker genes and number of selected marker genes as in (b)