mbkmeans

This is the development version of mbkmeans; for the stable release version, see mbkmeans.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

Mini-batch K-means Clustering for Single-Cell RNA-seq

Bioconductor version: Development (3.24)

Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.

Author: Yuwei Ni [aut, cph], Davide Risso [aut, cre, cph], Stephanie Hicks [aut, cph], Elizabeth Purdom [aut, cph]

Maintainer: Davide Risso <risso.davide at gmail.com>

Citation (from within R, enter citation("mbkmeans")):

Yuwei Ni, Davide Risso, Stephanie Hicks, Elizabeth Purdom. mbkmeans: Mini-batch K-means Clustering for Single-Cell RNA-seq. doi:10.18129/B9.bioc.mbkmeans, R package version 1.29.0, https://bioconductor.org/packages/mbkmeans.

Generated from the package metadata; it may differ from the package's own citation.

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("mbkmeans")

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("mbkmeans")

mbkmeans vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.29.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel
System Requirements	C++11
URL
Bug Reports	https://github.com/drisso/mbkmeans/issues

Suggests	beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown
Linking To	Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Enhances
Depends On Me
Imports Me	clusterExperiment
Suggests Me	bluster, concordexR, scDblFinder
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mbkmeans_1.29.0.tar.gz
Windows Binary (x86_64)	mbkmeans_1.29.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	mbkmeans_1.29.0.tgz
macOS Binary (sonoma-arm64)	mbkmeans_1.29.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mbkmeans
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mbkmeans
Package Short Url	https://bioconductor.org/packages/mbkmeans/
Package Downloads Report	Download Stats