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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

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
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
macOS Binary (x86_64) mbkmeans_1.19.0.tgz
macOS Binary (arm64)
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