mbkmeans

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

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

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DOI: 10.18129/B9.bioc.mbkmeans

Bioconductor version: Development (3.23)

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")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 1.27.0

In Bioconductor since BioC 3.9 (R-3.6) (6.5 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 OSCA.basic

Imports Me clusterExperiment

Suggests Me bluster, concordexR, scDblFinder

Links To Me

Build Report Build Report

Package Archives

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

Source Package mbkmeans_1.27.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64) mbkmeans_1.27.0.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/

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