dandelionR

This is the released version of dandelionR; for the devel version, see dandelionR.

Single-cell Immune Repertoire Trajectory Analysis in R

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DOI: 10.18129/B9.bioc.dandelionR

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0009-0005-9170-7881 , Nicholas Borcherding [aut] ORCID iD ORCID: 0000-0003-1427-6342 , Kelvin Tuong [aut, cre] ORCID iD ORCID: 0000-0002-6735-6808

Maintainer: Kelvin Tuong <z.tuong at uq.edu.au>

Citation (from within R, enter citation("dandelionR")):

Installation

To install this package, start R (version "4.5") 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 HTML R Script

Single-cell immune repertoire trajectory analysis with dandelionR and slingshot HTML R Script

vignette_reproduce_original.html HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, SingleCell, Software

Version 1.2.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 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

Suggests BiocStyle, fields, knitr, rmarkdown, RColorBrewer, scater, scRepertoire, DelayedMatrixStats, slingshot, testthat

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package dandelionR_1.2.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64) dandelionR_1.2.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/dandelionR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dandelionR

Bioc Package Browser https://code.bioconductor.org/browse/dandelionR/

Package Short Url https://bioconductor.org/packages/dandelionR/

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