Package: BayesSpace 1.23.0

Senbai Kang

BayesSpace: Clustering and Resolution Enhancement of Spatial Transcriptomes

Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Authors:Edward Zhao [aut], Senbai Kang [aut, cre], Matt Stone [aut], Xing Ren [ctb], Raphael Gottardo [ctb]

BayesSpace_1.23.0.tar.gz
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BayesSpace_1.23.0.tgz(r-4.6-x86_64)BayesSpace_1.23.0.tgz(r-4.6-arm64)BayesSpace_1.23.0.tgz(r-4.5-x86_64)BayesSpace_1.23.0.tgz(r-4.5-arm64)
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BayesSpace_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BayesSpace/json (API)
NEWS

# Install 'BayesSpace' in R:
install.packages('BayesSpace', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/edward130603/bayesspace/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On BioConductor:BayesSpace-1.23.0(bioc 3.24)BayesSpace-1.22.0(bioc 3.23)

softwareclusteringtranscriptomicsgeneexpressionsinglecellimmunooncologydataimportopenblascppopenmp

9.59 score 179 stars 1 packages 398 scripts 903 downloads 18 exports 139 dependencies

Last updated from:0411308424. Checks:1 NOTE, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE319
linux-devel-arm64WARNING468
linux-devel-x86_64WARNING527
source / vignettesOK511
linux-release-arm64WARNING425
linux-release-x86_64WARNING534
macos-release-arm64WARNING336
macos-release-x86_64WARNING609
macos-oldrel-arm64WARNING385
macos-oldrel-x86_64WARNING725
windows-develWARNING1185
windows-releaseWARNING1067
windows-oldrelWARNING1093
wasm-releaseOK250

Exports:adjustClusterLabelsclusterPlotcoreTunecounts2h5enhanceFeaturesexampleSCEfeaturePlotgetRDSmcmcChainparaLapplyqPlotqTuneread10Xh5readVisiumremoveChainspatialClusterspatialEnhancespatialPreprocess

Dependencies:abindarrowaskpassassertthatassortheadbase64encbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocNeighborsBiocParallelBiocSingularbitbit64bitopsblobblustercachemCairocliclustercodacodetoolscpp11curldata.tableDBIdbplyrDelayedArraydigestdir.expiryDirichletRegdplyrdqrngedgeRfarverfastmapfilelockFNNformatRFormulafutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttr2igraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmaxLikmclustmemoisemetapodmicrobenchmarkmiscToolsopensslpheatmappillarpkgconfigpngpurrrR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppDistRcppEigenRcppMLRcppProgressRCurlrhdf5rhdf5filtersRhdf5librjsonrlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorsS7sandwichScaledMatrixscalesscaterscranscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectutf8uwotvctrsviporviridisviridisLitewithrxgboostXVectorzoo

BayesSpace

Edward Zhao, Matt Stone, Xing Ren, and Raphael Gottardo

Rendered fromBayesSpace.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-06-17
Started: 2020-07-07