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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. 7 — Case studies scrutinizing Scanpy and Seurat. a Gene rank vs log fold-change values for the Scanpy Wilcoxon (with tie correction, ranking by the absolute value of the score) and Seurat Wilcoxon methods for the Oligodendrocyte cell type cluster in the Zeisel dataset. The color of the point indicates whether or not the gene has an exactly zero p-value. b The proportion of top 20 genes shared between methods implemented in Scanpy and Seurat and the method of ranking genes by the raw log fold-change calculation on simulated datasets with increasing number of total cells. These simulations have parameters estimated from the pbmc3k dataset and a location parameter for the DE factor of 3. c Visualization of difference in rankings between the Scanpy t method (ranking by the absolute value of the score) and Seurat’s t-test method on the B cell cluster in the pbmc3k dataset. d Scatter plot between the log fold-change values calculated by Seurat and Scanpy on the B cell cluster in the pbmc3k dataset