Package: mbkmeans 1.28.0
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:
mbkmeans_1.28.0.tar.gz
mbkmeans_1.28.0.zip(r-4.7)mbkmeans_1.28.0.zip(r-4.6)
mbkmeans_1.28.0.tgz(r-4.6-x86_64)mbkmeans_1.28.0.tgz(r-4.6-arm64)mbkmeans_1.26.0.tgz(r-4.5-x86_64)mbkmeans_1.26.0.tgz(r-4.5-arm64)
mbkmeans_1.28.0.tar.gz(r-4.7-arm64)mbkmeans_1.28.0.tar.gz(r-4.7-x86_64)mbkmeans_1.28.0.tar.gz(r-4.6-arm64)mbkmeans_1.28.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
mbkmeans/json (API)
NEWS
| # Install 'mbkmeans' in R: |
| install.packages('mbkmeans', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/drisso/mbkmeans/issues
On BioConductor:mbkmeans-1.29.0(bioc 3.24)mbkmeans-1.28.0(bioc 3.23)
clusteringgeneexpressionrnaseqsoftwaretranscriptomicssequencingsinglecellhuman-cell-atlasopenblascpp
Last updated from:a415e0d264 (on RELEASE_3_23). Checks:1 WARNING, 8 NOTE, 1 OK, 4 FAIL. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 247 | ||
| linux-devel-arm64 | NOTE | 391 | ||
| linux-devel-x86_64 | NOTE | 469 | ||
| source / vignettes | OK | 453 | ||
| linux-release-arm64 | NOTE | 390 | ||
| linux-release-x86_64 | NOTE | 503 | ||
| macos-release-arm64 | NOTE | 321 | ||
| macos-release-x86_64 | NOTE | 697 | ||
| macos-oldrel-arm64 | FAIL | 89 | ||
| macos-oldrel-x86_64 | FAIL | 174 | ||
| windows-devel | NOTE | 604 | ||
| windows-release | NOTE | 653 | ||
| windows-oldrel | FAIL | 291 | ||
| wasm-release | FAIL | 171 |
Exports:blocksizecompute_wcssmbkmeansMbkmeansParammini_batchpredict_mini_batchpredict_mini_batch_r
Dependencies:abindaskpassassortheadbeachmatbenchmarkmebenchmarkmeDataBHBiobaseBiocGenericsbiocmakeBiocParallelcliClusterRcodetoolscpp11curlDelayedArraydir.expirydoParalleldplyrfarverfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegmpgtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigR6RColorBrewerRcppRcppArmadilloRhdf5librlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectutf8vctrsviridisLitewithrXVector
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 |
