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Cell-connectivity-guided trajectory inference from single-cell data

MOTIVATION: Single-cell RNA-sequencing enables cell-level investigation of cell differentiation, which can be modelled using trajectory inference methods. While tremendous effort has been put into designing these methods, inferring accurate trajectories automatically remains difficult. Therefore, th...

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Detalles Bibliográficos
Autores principales: Smolander, Johannes, Junttila, Sini, Elo, Laura L
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10474950/
https://www.ncbi.nlm.nih.gov/pubmed/37624916
http://dx.doi.org/10.1093/bioinformatics/btad515
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author Smolander, Johannes
Junttila, Sini
Elo, Laura L
author_facet Smolander, Johannes
Junttila, Sini
Elo, Laura L
author_sort Smolander, Johannes
collection PubMed
description MOTIVATION: Single-cell RNA-sequencing enables cell-level investigation of cell differentiation, which can be modelled using trajectory inference methods. While tremendous effort has been put into designing these methods, inferring accurate trajectories automatically remains difficult. Therefore, the standard approach involves testing different trajectory inference methods and picking the trajectory giving the most biologically sensible model. As the default parameters are often suboptimal, their tuning requires methodological expertise. RESULTS: We introduce Totem, an open-source, easy-to-use R package designed to facilitate inference of tree-shaped trajectories from single-cell data. Totem generates a large number of clustering results, estimates their topologies as minimum spanning trees, and uses them to measure the connectivity of the cells. Besides automatic selection of an appropriate trajectory, cell connectivity enables to visually pinpoint branching points and milestones relevant to the trajectory. Furthermore, testing different trajectories with Totem is fast, easy, and does not require in-depth methodological knowledge. AVAILABILITY AND IMPLEMENTATION: Totem is available as an R package at https://github.com/elolab/Totem.
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spelling pubmed-104749502023-09-03 Cell-connectivity-guided trajectory inference from single-cell data Smolander, Johannes Junttila, Sini Elo, Laura L Bioinformatics Original Paper MOTIVATION: Single-cell RNA-sequencing enables cell-level investigation of cell differentiation, which can be modelled using trajectory inference methods. While tremendous effort has been put into designing these methods, inferring accurate trajectories automatically remains difficult. Therefore, the standard approach involves testing different trajectory inference methods and picking the trajectory giving the most biologically sensible model. As the default parameters are often suboptimal, their tuning requires methodological expertise. RESULTS: We introduce Totem, an open-source, easy-to-use R package designed to facilitate inference of tree-shaped trajectories from single-cell data. Totem generates a large number of clustering results, estimates their topologies as minimum spanning trees, and uses them to measure the connectivity of the cells. Besides automatic selection of an appropriate trajectory, cell connectivity enables to visually pinpoint branching points and milestones relevant to the trajectory. Furthermore, testing different trajectories with Totem is fast, easy, and does not require in-depth methodological knowledge. AVAILABILITY AND IMPLEMENTATION: Totem is available as an R package at https://github.com/elolab/Totem. Oxford University Press 2023-08-25 /pmc/articles/PMC10474950/ /pubmed/37624916 http://dx.doi.org/10.1093/bioinformatics/btad515 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Paper
Smolander, Johannes
Junttila, Sini
Elo, Laura L
Cell-connectivity-guided trajectory inference from single-cell data
title Cell-connectivity-guided trajectory inference from single-cell data
title_full Cell-connectivity-guided trajectory inference from single-cell data
title_fullStr Cell-connectivity-guided trajectory inference from single-cell data
title_full_unstemmed Cell-connectivity-guided trajectory inference from single-cell data
title_short Cell-connectivity-guided trajectory inference from single-cell data
title_sort cell-connectivity-guided trajectory inference from single-cell data
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10474950/
https://www.ncbi.nlm.nih.gov/pubmed/37624916
http://dx.doi.org/10.1093/bioinformatics/btad515
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