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Bioconductor - mbkmeans (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics Version 1.25.0 In Bioconductor since BioC 3.9 (R-3.6) (6 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, concordexR, scDblFinder Links To Me Build Report Build Report Package Archives

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

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