Dune
This is the development version of Dune; for the stable release version, see Dune.
Improving replicability in single-cell RNA-Seq cell type discovery
Bioconductor version: Development (3.24)
Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.
Author: Hector Roux de Bezieux [aut, cre]
, Kelly Street [aut]
Maintainer: Hector Roux de Bezieux <hector.rouxdebezieux at berkeley.edu>
citation("Dune")):
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("Dune")
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("Dune")| Dune Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6) |
| Imports | BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr, tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat (>= 2.1.0) |
| 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 | Dune_1.25.0.tar.gz |
| Windows Binary (x86_64) | Dune_1.25.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Dune_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/Dune |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Dune |
| Bioc Package Browser | https://code.bioconductor.org/browse/Dune/ |
| Package Short Url | https://bioconductor.org/packages/Dune/ |
| Package Downloads Report | Download Stats |