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bioRxiv · 10.1101/2025.02.04.636146

dandelionR: Single-cell immune repertoire trajectory analysis in R

Yu, J.·Xu, X.·Borcherding, N.·Tuong, Z. K.
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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 Dandelions 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.

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Yu, J., Xu, X., Borcherding, N., Tuong, Z. K.. 2025-02-07. dandelionR: Single-cell immune repertoire trajectory analysis in R. https://doi.org/10.1101/2025.02.04.636146

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