# dandelionR: Single-cell immune repertoire trajectory analysis in R

## TL;DR

dandelionR is an R package that enables the analysis of immune cell development using single-cell RNA and receptor sequencing data.

## Contribution

dandelionR provides an R-based implementation of the VDJ-feature space method for trajectory analysis.

## Key findings

- dandelionR integrates scRNA-seq and scVDJ-seq data using diffusion maps and absorbing Markov chains.
- The package offers a new option for R users to analyze immune repertoire trajectories.
- It replicates the workflow of the Python-based Dandelion package 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 the VDJ-feature space method, which addresses the challenge of integrating single-cell AIR data with gene expression data and enhances 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 maps and absorbing Markov chains to R, offering a new option for scRNA-seq and scVDJ-seq analysis to R users.