dandelionR
This is the released version of dandelionR; for the devel version, see dandelionR.
Single-cell Immune Repertoire Trajectory Analysis in R
Bioconductor version: Release (3.23)
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("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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dandelionR")| Single-cell immune repertoire trajectory analysis with dandelionR and slingshot | HTML | R Script |
| Single-cell immune repertoire trajectory analysis with dandelionR | HTML | R Script |
| vignette_reproduce_original.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology, SingleCell, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods, miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam, stats, SummarizedExperiment, uwot, RANN |
| System Requirements | |
| URL | https://www.github.com/tuonglab/dandelionR/ |
| Bug Reports | https://www.github.com/tuonglab/dandelionR/issues |
See More
| Suggests | BiocStyle, fields, knitr, rmarkdown, RColorBrewer, scater, scRepertoire, DelayedMatrixStats, slingshot, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | dandelionR_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | 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 Short Url | https://bioconductor.org/packages/dandelionR/ |
| Package Downloads Report | Download Stats |