mbkmeans

DOI: 10.18129/B9.bioc.mbkmeans  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

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

Details

biocViews	Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel
LinkingTo	Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Suggests	beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown
SystemRequirements	C++11
Enhances
URL
BugReports	https://github.com/drisso/mbkmeans/issues
Depends On Me	OSCA.basic
Imports Me	clusterExperiment
Suggests Me	bluster, scDblFinder
Links To Me
Build Report

Package Archives

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

Source Package	mbkmeans_1.14.0.tar.gz
Windows Binary	mbkmeans_1.14.0.zip
macOS Binary (x86_64)	mbkmeans_1.14.0.tgz
macOS Binary (arm64)	mbkmeans_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mbkmeans
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mbkmeans
Bioc Package Browser	https://code.bioconductor.org/browse/mbkmeans/
Package Short Url	https://bioconductor.org/packages/mbkmeans/
Package Downloads Report	Download Stats