Package: mbkmeans 1.23.0

Davide Risso

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

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

Authors:Yuwei Ni [aut, cph], Davide Risso [aut, cre, cph], Stephanie Hicks [aut, cph], Elizabeth Purdom [aut, cph]

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mbkmeans.pdf |mbkmeans.html✨
mbkmeans/json (API)
NEWS

# Install 'mbkmeans' in R:

install.packages('mbkmeans', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/drisso/mbkmeans/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:mbkmeans-1.23.0(bioc 3.21)mbkmeans-1.22.0(bioc 3.20)

clustering geneexpression rnaseq software transcriptomics sequencing singlecell human-cell-atlas cpp

7.37 score 9 stars 2 packages 54 scripts 834 downloads 2 mentions 7 exports 80 dependencies

Last updated 2 months agofrom:446bb72750. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 10 2024
R-4.5-win-x86_64	NOTE	Dec 10 2024
R-4.5-linux-x86_64	NOTE	Dec 10 2024
R-4.4-win-x86_64	NOTE	Dec 10 2024
R-4.4-mac-x86_64	NOTE	Dec 10 2024
R-4.4-mac-aarch64	NOTE	Dec 10 2024
R-4.3-win-x86_64	NOTE	Dec 10 2024
R-4.3-mac-x86_64	NOTE	Dec 10 2024
R-4.3-mac-aarch64	NOTE	Dec 10 2024

Exports:blocksize compute_wcss mbkmeans MbkmeansParam mini_batch predict_mini_batch predict_mini_batch_r

Dependencies:abind askpass assorthead beachmat benchmarkme benchmarkmeData BH Biobase BiocGenerics BiocParallel cli ClusterR codetools colorspace cpp11 crayon curl DelayedArray doParallel dplyr fansi farver foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gmp gtable httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo Rhdf5lib rlang S4Arrays S4Vectors scales SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

An introduction to mbkmeans

Yuwei Ni, Davide Risso, Stephanie Hicks, and Elizabeth Purdom

Rendered fromVignette.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2021-01-19
Started: 2018-11-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
blocksize	blocksize
Cluster rows of a matrix	clusterRows
Compute Whithin-Cluster Sum of Squares	compute_wcss
Mini-Batch k-means for large single cell sequencing data	mbkmeans mbkmeans,ANY-method mbkmeans,LinearEmbeddingMatrix-method mbkmeans,SingleCellExperiment-method mbkmeans,SummarizedExperiment-method
Mini-batch k-means clustering	MbkmeansParam show,MbkmeansParam-method
Mini_batch	mini_batch
Predict_mini_batch	predict_mini_batch
Compute labels for mini-batch k-means	predict_mini_batch_r

Usage by other packages (reverse dependencies)