bluster
This is the released version of bluster; for the devel version, see bluster.
Clustering Algorithms for Bioconductor
Bioconductor version: Release (3.23)
Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.
Author: Aaron Lun [aut, cre], Stephanie Hicks [ctb], Basil Courbayre [ctb], Tuomas Borman [ctb], Leo Lahti [ctb]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("bluster")):
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("bluster")
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("bluster")| 1. Clustering algorithms | HTML | R Script |
| 2. Clustering diagnostics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneExpression, ImmunoOncology, SingleCell, Software, Transcriptomics |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | |
| Imports | stats, methods, utils, cluster, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors |
| System Requirements | C++17 |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster |
| Linking To | Rcpp, assorthead |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, scrapbook, SingleRBook |
| Imports Me | BatChef, chevreulProcess, clustSIGNAL, concordexR, dandelionR, jvecfor, mia, miaDash, MPAC, poem, scDblFinder, scDiagnostics, scran, scTypeEval, Voyager, Canek |
| Suggests Me | anglemania, batchelor, ChromSCape, Coralysis, dittoSeq, GSVA, Ibex, mbkmeans, miaViz, MOSim, mumosa, scLANE, sketchR, spatialHeatmap, SuperCellCyto, OMA, SuperCell |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | bluster_1.22.0.tar.gz |
| Windows Binary (x86_64) | bluster_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | bluster_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | bluster_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/bluster |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/bluster |
| Bioc Package Browser | https://code.bioconductor.org/browse/bluster/ |
| Package Short Url | https://bioconductor.org/packages/bluster/ |
| Package Downloads Report | Download Stats |