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. 2023 Jun 23;24:149. doi: 10.1186/s13059-023-02988-9

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© The Author(s) 2023

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. 6 — Application of scTour to human skeletal muscle development. a scTour’s latent space-based UMAP visualization of the cell types from all stages during human limb development (58,021 cells) [34]. Limb.Mesen, limb mesenchymal cells; PreChondro, prechondrogenic cells; Chondro, chondrogenic cells; Dermal, dermal fibroblasts; SkM, skeletal muscle cells; MSC, mesenchymal stromal cells; Teno, tenogenic cells; FAPs, fibro-adipogenic progenitors; SMC, smooth muscle cells. b As in a, but colored by the pseudotime estimated by scTour. c UMAP plots displaying cells from each of the developmental stages represented by different colors. d scTour’s latent space-based UMAP representations of the skeletal muscle progenitor and stem cells collected across prenatal and postnatal development (4816 cells), with colors indicating pseudotime estimates from scTour (left) and real developmental stages (right). e Heatmap illustrating the expression dynamics of top 100 most significant genes along the developmental trajectory. Developmental stages and estimated pseudotime are displayed on top. f Ordering of the in vivo skeletal muscle progenitor and stem cells based on the inferred pseudotime (upper), and ordering of the in vitro hPSC-derived progenitors based on the predicted pseudotime (lower). Dots denote the median values. Colors represent the developmental stages as in d (upper) and directed differentiation protocols and time points (lower)