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. 2021 Apr 29;22:124. doi: 10.1186/s13059-021-02341-y

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© The Author(s) 2021

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 — Application of PseudotimeDE, tradeSeq, and Monocle3-DE to the LPS-dendritic cell dataset. Left panels a–d are based on pseudotime inferred by Slingshot; right panels e–h are based on pseudotime inferred by Monocle3-PI. a, e Histograms of all genes’ p-values by the three DE methods. The bimodal distributions of tradeSeq’s p-values suggest a violation of the requirement that p-values follow the Uniform [0,1] distribution under the null hypothesis. b, f Venn plots showing the overlaps of the significant DE genes (BH adjusted- p≤0.01) identified by the three DE methods. PseudotimeDE’s DE genes almost include tradeSeq’s. c, g Numbers of GO terms enriched (p<0.01) in the significant DE genes specifically found by PseudotimeDE or tradeSeq/Monocle3-DE in pairwise comparisons between PseudotimeDE and tradeSeq/Monocle3-DE in b and f. Many more GO terms are enriched in the PseudotimeDE-specific DE genes than in the tradeSeq- or Monocle3-DE-specific ones. d, h Example GO terms enriched in the Pseudotime-specific DE genes in c and g. Many of these terms are related to LPS, immune process, and defense to bacterium