dandelionR
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dandelionR")Details
| Maintainer | Kelvin Tuong <z.tuong@uq.edu.au> |
| Author | Jiawei Yu [aut] (ORCID: <https://orcid.org/0009-0005-9170-7881>), Nicholas Borcherding [aut] (ORCID: <https://orcid.org/0000-0003-1427-6342>), Kelvin Tuong [aut, cre] (ORCID: <https://orcid.org/0000-0002-6735-6808>) |
| License | MIT + file LICENSE |
| URL | https://www.github.com/tuonglab/dandelionR/ |
| Bug Reports | https://www.github.com/tuonglab/dandelionR/issues |
| Downloads rank | 145 |
| Source branch | RELEASE_3_23 |
| biocViews | ImmunoOncology, SingleCell, Software |
Documentation
- Reproducing the original dandelion method/paper
- Single-cell immune repertoire trajectory analysis with dandelionR
- Single-cell immune repertoire trajectory analysis with dandelionR and slingshot
Download
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