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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology, SingleCell, Software |
| Version | 1.5.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dandelionR_1.5.0.tar.gz |
| Windows Binary (x86_64) | dandelionR_1.5.0.zip |
| macOS Binary (big-sur-x86_64) | dandelionR_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | dandelionR_1.5.0.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 |