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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


Bioconductor version: Development (3.19)

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 "4.4") 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

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (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
See More
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, scDblFinder
Links To Me
Build Report Build Report

Package Archives

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

Source Package mbkmeans_1.19.0.tar.gz
Windows Binary mbkmeans_1.19.0.zip (64-bit only)
macOS Binary (x86_64) mbkmeans_1.19.0.tgz
macOS Binary (arm64) mbkmeans_1.19.0.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