Single-cell Immune Repertoire Trajectory Analysis in R • dandelionR

Welcome to dandelionR!

dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation in dandelion.

It provides all the necessary tools to interface with scRepertoire and a custom implementation of absorbing markov chain for pseudotime inference, inspired based on the palantir python package.

Installation from Bioconductor

You can install dandelionR from Bioconductor with:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version="devel")

BiocManager::install("dandelionR")

Installation from GitHub

You can install dandelionR from GitHub with:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github('tuonglab/dandelionR', dependencies = TRUE)

Quick Start

library(dandelionR)

This is a work in progress, so please feel free to open an issue if you encounter any problems or have any suggestions for improvement.

Citation

If you use dandelionR in your work, you can cite our manuscript on bioRxiv:

Yu, J., Borcherding, N. & Tuong, Z.K.. (2025) DandelionR: Single-cell immune repertoire trajectory analysis in R. bioRxiv 2025.02.04.636146. https://doi.org/10.1101/2025.02.04.636146

Please also cite the original dandelion paper:

Suo, C. et al. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nat. Biotechnol. 42, 40-51 (2024). https://doi.org:10.1038/s41587-023-01734-7