DuoClustering2018
This is the released version of DuoClustering2018; for the devel version, see DuoClustering2018.
Data, Clustering Results and Visualization Functions From Duò et al (2018)
Bioconductor version: Release (3.23)
Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance.
Author: Angelo Duò, Charlotte Soneson
Maintainer: Angelo Duò <angelo.duo at icloud.com>
citation("DuoClustering2018")):
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")
BiocManager::install("DuoClustering2018")
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("DuoClustering2018")| Apply clustering method | HTML | R Script |
| Plot performance summaries | HTML | R Script |
| Visualize data sets and clustering results with iSEE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, SingleCellData |
| Version | 1.30.0 |
| License | GPL (>=2) |
| Depends | |
| Imports | ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2, purrr, reshape2, viridis, ggthemes, stats, methods |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | corral, scry |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DuoClustering2018_1.30.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/DuoClustering2018 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DuoClustering2018 |
| Package Short Url | https://bioconductor.org/packages/DuoClustering2018/ |
| Package Downloads Report | Download Stats |