mbkmeans
Mini-batch K-means Clustering for Single-Cell RNA-seq
Bioconductor version: Release (3.17)
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 "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6) |
| Imports | methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel |
| Linking To | Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR |
| Suggests | beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown |
| System Requirements | C++11 |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/drisso/mbkmeans/issues |
See More
| Depends On Me | OSCA.basic |
| Imports Me | clusterExperiment |
| Suggests Me | bluster, scDblFinder |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mbkmeans_1.16.0.tar.gz |
| Windows Binary | mbkmeans_1.16.0.zip |
| macOS Binary (x86_64) | mbkmeans_1.16.0.tgz |
| macOS Binary (arm64) | mbkmeans_1.16.0.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 |