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. 2024 Jan 27;15:833. doi: 10.1038/s41467-024-44823-0

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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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — Alternate analyses. Using monocle3 to infer the trajectory also yields a single-lineage trajectory (a), albeit different than the one inferred by slingshot. After inferring the trajectory with monocle3, there is also differential progression: the pseudotime distributions along the trajectory are not identical and we indeed reject the null hypothesis using the progressionTest. On the other hand, while DAseq (b) and milo (c) correctly identify that there is differential abundance, their results are much harder to interpret.