mbkmeans

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

Bioconductor version: 3.23 · Package version: 1.28.0

Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.

Installation

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

BiocManager::install("mbkmeans")

Maintainer	Davide Risso <risso.davide@gmail.com>
Author	Yuwei Ni [aut, cph], Davide Risso [aut, cre, cph], Stephanie Hicks [aut, cph], Elizabeth Purdom [aut, cph]
License	MIT + file LICENSE
Bug Reports	https://github.com/drisso/mbkmeans/issues
System Requirements	C++11
Downloads rank	907
Source branch	RELEASE_3_23
biocViews	Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Dependencies

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

Reverse dependencies

Imports Me (1): clusterExperiment

Suggests Me (3): bluster, concordexR, scDblFinder