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

Johannes Smolander1, Sini Junttila1, Laura L Elo1,2

  • 1Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland.

Bioinformatics (Oxford, England)
|August 25, 2023
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Summary
This summary is machine-generated.

Totem, an R package, simplifies cell differentiation trajectory inference from single-cell RNA sequencing data. It automatically selects optimal tree-shaped trajectories and identifies key cellular branching points, reducing the need for extensive methodological expertise.

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Area of Science:

  • Computational Biology
  • Genomics
  • Bioinformatics

Background:

  • Single-cell RNA sequencing (scRNA-seq) provides high-resolution data for studying cellular processes like differentiation.
  • Trajectory inference methods are crucial for modeling cell differentiation but often require manual selection and parameter tuning.
  • Accurate trajectory inference is challenging due to the complexity of biological systems and data variability.

Purpose of the Study:

  • To introduce Totem, an open-source R package for automated inference of tree-shaped trajectories from scRNA-seq data.
  • To provide an easy-to-use tool that reduces the methodological expertise needed for trajectory analysis.
  • To enable efficient identification of branching points and milestones in cellular differentiation.

Main Methods:

  • Totem generates numerous clustering results and estimates their topologies using minimum spanning trees.
  • Cell connectivity is calculated to assess the robustness and relationships between inferred trajectories.
  • The package facilitates automatic selection of the most biologically plausible trajectory.

Main Results:

  • Totem automates the selection of tree-shaped trajectories from single-cell data.
  • Cell connectivity analysis aids in visually identifying critical branching points and developmental milestones.
  • The R package offers a fast and user-friendly approach to trajectory inference, minimizing the need for deep methodological knowledge.

Conclusions:

  • Totem streamlines the analysis of cell differentiation trajectories from scRNA-seq data.
  • The package enhances the interpretability of differentiation processes by highlighting key cellular events.
  • Totem democratizes advanced trajectory inference techniques for a wider range of researchers.