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# 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`](https://www.github.com/zktuong/dandelion).
It provides all the necessary tools to interface with [`scRepertoire`](https://github.com/ncborcherding/scRepertoire) and a custom implementation of absorbing markov chain for pseudotime inference, inspired based on the [palantir](https://github.com/dpeerlab/Palantir) python package.
## Installation from Bioconductor
You can install `dandelionR` from Bioconductor with:
```R
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# If installing from Bioc devel, do this first:
# BiocManager::install(version="devel")
BiocManager::install("dandelionR")
```
## Installation from GitHub
You can install `dandelionR` from GitHub with:
```R
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github('tuonglab/dandelionR', dependencies = TRUE)
```
## Quick Start
```R
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 published in the [Computational and Structural Biotechnology Journal](https://authors.elsevier.com/sd/article/S2001-0370(25)00263-6):
```
Yu, J., Xu, X., Borcherding, N., Tuong, Z.K. dandelionR: Single-cell immune repertoire trajectory analysis in R. Comput. Struct. Biotechnol. J. (2025). doi:10.1016/j.csbj.2025.06.047.
```
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). doi:10.1038/s41587-023-01734-7
```
