Journal Article

A robust and accurate single-cell data trajectory inference method using ensemble pseudotime

Harris, Frederick C., Nguyen, Tin, Tran, Duc, Dascalu, Sergiu M., Zhang, Yifan

2023

Overview

Background The advance in single-cell RNA sequencing technology has enhanced the analysis of cell development by profiling heterogeneous cells in individual cell resolution. In recent years, many trajectory inference methods have been developed. They have focused on using the graph method to infer the trajectory using single-cell data, and then calculate the geodesic distance as the pseudotime. However, these methods are vulnerable to errors caused by the inferred trajectory. Therefore, the calculated pseudotime suffers from such errors. Results We proposed a novel framework for trajectory inference called the s ingle- c ell data T rajectory inference method using E nsemble P seudotime inference (scTEP). scTEP utilizes multiple clustering results to infer robust pseudotime and then uses the pseudotime to fine-tune the learned trajectory. We evaluated the scTEP using 41 real scRNA-seq data sets, all of which had the ground truth development trajectory. We compared the scTEP with state-of-the-art methods using the aforementioned data sets. Experiments on real linear and non-linear data sets demonstrate that our scTEP performed superior on more data sets than any other method. The scTEP also achieved a higher average and lower variance on most metrics than other state-of-the-art methods. In terms of trajectory inference capacity, the scTEP outperforms those methods. In addition, the scTEP is more robust to the unavoidable errors resulting from clustering and dimension reduction. Conclusion The scTEP demonstrates that utilizing multiple clustering results for the pseudotime inference procedure enhances its robustness. Furthermore, robust pseudotime strengthens the accuracy of trajectory inference, which is the most crucial component in the pipeline. scTEP is available at https://cran.r-project.org/package=scTEP .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accuracy / Algorithms / Benchmarking / Bioinformatics / Biomedical and Life Sciences / Cells / Cluster Analysis / Clustering / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Datasets / Electronic data processing / Errors / Gene expression / Gene Expression Profiling - methods / Gene sequencing / Inference / Life Sciences / Mathematical analysis / Methods / Microarrays / Pathway / Performance evaluation / Pseudotime / RNA sequencing / Robustness / Sequence Analysis, RNA - methods / Single cell / Single-Cell Analysis - methods / Software / State of the art / Trajectory analysis / Trajectory inference