dandelionR

This is the development version of dandelionR; for the stable release version, see dandelionR.

Single-cell Immune Repertoire Trajectory Analysis in R

Bioconductor version: Development (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: 0009-0005-9170-7881 , Nicholas Borcherding [aut] ORCID: 0000-0003-1427-6342 , Kelvin Tuong [aut, cre] 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("dandelionR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, SingleCell, Software
Version	1.1.5
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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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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