https://github.com/drisso/mbkmeans

K-means clustering for large single-cell datasets
https://github.com/drisso/mbkmeans

clustering human-cell-atlas

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K-means clustering for large single-cell datasets

• Host: GitHub
• URL: https://github.com/drisso/mbkmeans
• Owner: drisso
• License: mit
• Created: 2018-04-18T15:34:11.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2022-03-22T17:22:59.000Z (over 3 years ago)
• Last Synced: 2024-12-17T13:51:37.354Z (10 months ago)
• Topics: clustering, human-cell-atlas
• Language: R
• Homepage:
• Size: 5.89 MB
• Stars: 10
• Watchers: 4
• Forks: 3
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# mbkmeans: Mini-batch k-means clustering for single-cell RNA-seq

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

[![BioC release](http://www.bioconductor.org/shields/build/release/bioc/mbkmeans.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/mbkmeans)

[![BioC devel](http://www.bioconductor.org/shields/build/release/bioc/mbkmeans.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/mbkmeans)

[![R-CMD-check](https://github.com/drisso/mbkmeans/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/drisso/mbkmeans/actions)

This package implements the mini-batch k-means algorithm for large datasets, 

including support for on-disk data representation.

The method is described in details in the paper:

[S. Hicks, R. Liu, Y. Ni, E. Purdom, D. Risso (2021).

mbkmeans: Fast clustering for single cell data using mini-batch k-means. PLOS Computational Biology.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008625)

## Installation

In virtually all cases, installing from Bioconductor is recommended.

```{r}

if (!requireNamespace("BiocManager", quietly=TRUE))

    install.packages("BiocManager")

BiocManager::install("mbkmeans")

```

In the rare event you need the development version from GitHub, use the following.

```{r}

library(devtools)

BiocManager::install("drisso/mbkmeans")

```