dandelionR
This is the released version of dandelionR; for the devel version, see dandelionR.
All Bioconductor versions of dandelionR
3.24 (devel), 3.23 (release), 3.22, 3.21
Single-cell Immune Repertoire Trajectory Analysis in R
Bioconductor version: 3.23 · Package version: 1.4.0
dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.
Author: Jiawei Yu [aut] 
, Nicholas Borcherding [aut] , Kelvin Tuong [aut, cre]
Maintainer: Kelvin Tuong <z.tuong at uq.edu.au>
Citation
From within R, enter citation("dandelionR"):
Jiawei Yu, Nicholas Borcherding, Kelvin Tuong. dandelionR: Single-cell Immune Repertoire Trajectory Analysis in R. doi:10.18129/B9.bioc.dandelionR, R package version 1.4.0, https://bioconductor.org/packages/dandelionR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dandelionR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.4.0 |
| License | MIT + file LICENSE |
| URL | https://www.github.com/tuonglab/dandelionR/ |
| Bug Reports | https://www.github.com/tuonglab/dandelionR/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 2277 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ImmunoOncology, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/dandelionR/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dandelionR")| Reproducing the original dandelion method/paper | HTML | R Script |
| Single-cell immune repertoire trajectory analysis with dandelionR | HTML | R Script |
| Single-cell immune repertoire trajectory analysis with dandelionR and slingshot | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | dandelionR_1.4.0.tar.gz |
| Windows binary (x86_64) | dandelionR_1.4.0.zip |
| macOS binary (arm64) | dandelionR_1.4.0.tgz |
| macOS binary (x86_64) | dandelionR_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dandelionR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dandelionR |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.4.0)
Imports: BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods, miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam, stats, SummarizedExperiment, uwot, RANN
Suggests: BiocStyle, fields, knitr, rmarkdown, RColorBrewer, scater, scRepertoire, DelayedMatrixStats, slingshot, testthat