Work

dandelionR : Single-cell immune repertoire trajectory analysis in R

Year: 2025

Type: article

Abstract: Integration of single-cell RNA-sequencing (scRNA-seq) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) is extremely powerful in studying lymphocyte development. A python-based package, Dandelion , introduced VDJ-feature space method, which addresses the challenge in integration of single-cell AIR data with gene expression data and enhanced the trajectory analysis results. However, no R-based equivalent or similar methods currently exist. To fill this gap, we present dandelionR , an R implementation of Dandelion ’s trajectory analysis workflow, bringing the VDJ feature space construction and trajectory analysis using diffusion map and absorbing Markov chain to R, offering a new option for scRNA-seq and scVDJ-seq analysis to R language users.

Source: Computational and Structural Biotechnology Journal

DOI: 10.1016/j.csbj.2025.06.047

Authors: Jiawei Yu, Xiaohan Xu, Nicholas Borcherding, Zewen Kelvin Tuong

Institutions: The University of Queensland, Washington University in St. Louis

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,230

Funder: Children's Hospital Foundation