mbkmeans

DOI: 10.18129/B9.bioc.mbkmeans    

This is the development version of mbkmeans; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script mbkmeans vignette
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.1.1
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports methods, DelayedArray, Rcpp, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix
LinkingTo Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Suggests beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, knitr, testthat
SystemRequirements C++11
Enhances
URL
BugReports https://github.com/drisso/mbkmeans/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package mbkmeans_1.1.1.tar.gz
Windows Binary mbkmeans_1.1.1.zip
Mac OS X 10.11 (El Capitan) mbkmeans_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/mbkmeans
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mbkmeans
Package Short Url https://bioconductor.org/packages/mbkmeans/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: