dandelionR: Single-cell immune repertoire trajectory analysis in R

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.