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dandelionR
This is thereleased version of dandelionR; for the devel version, seedandelionR.
Single-cell Immune Repertoire Trajectory Analysis in R
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: 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("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 appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology,SingleCell,Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | MIT + fileLICENSE |
| 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 |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | dandelionR_1.2.0.tar.gz |
| Windows Binary (x86_64) | dandelionR_1.2.0.zip |
| macOS Binary (x86_64) | dandelionR_1.2.0.tgz |
| 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/ |
| Package Downloads Report | Download Stats |