[](https://codecov.io/gh/tuonglab/dandelionR) [](https://github.com/tuonglab/dandelionR/actions/workflows/R-CMD-check.yml) [](https://github.com/tuonglab/dandelionR/actions/workflows/vignette.yml) # 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") # The following initializes usage of Bioc devel 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 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 ```