ArticleBioinformatics (Oxford, England)2023
Cell-connectivity-guided trajectory inference from single-cell data.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- iAODE for benchmarking and continuum modeling of single-cell chromatin accessibility.Communications biology · 2026Article
- Functionally Characterizing the Renal Cell Carcinoma Tumor-Immune Microenvironment via Patient-Derived Ex Vivo Models.Cancer research communications · 2026Article
- Molecular characterization of directly reprogrammed neurons from human fibroblasts using single cell RNA sequencing.Scientific reports · 2026Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- SPP1+ tumor-associated macrophages define a high-risk subgroup and inform personalized therapy in hepatocellular carcinoma.Frontiers in oncology · 2025Article
- Optimized network inference for immune diseased single cells.Frontiers in immunology · 2025Article
- Population-Level Cell Trajectory Inference Based on Gaussian Distributions.Biomolecules · 2024Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
- scCRT: a contrastive-based dimensionality reduction model for scRNA-seq trajectory inference.Briefings in bioinformatics · 2024Article
- Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference.Briefings in bioinformatics · 2024Article
- Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference.bioRxiv : the preprint server for biology · 2023Article
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3 authors.
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Abstract
motivationSingle-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.
resultsWe 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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