Preparing your experiment for BayesSpace | Loading data | Pre-processing data | Clustering | Selecting the number of clusters | Clustering with BayesSpace | Visualizing spatial clusters | Enhanced resolution | Clustering at enhanced resolution | Enhancing the resolution of gene expression | Visualizing enhanced gene expression | Accessing Markov chains
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:
BayesSpace_1.23.0.tar.gz
BayesSpace_1.23.0.zip(r-4.7)BayesSpace_1.23.0.zip(r-4.6)BayesSpace_1.23.0.zip(r-4.5)
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)
BayesSpace_1.23.0.tar.gz(r-4.7-arm64)BayesSpace_1.23.0.tar.gz(r-4.7-x86_64)BayesSpace_1.23.0.tar.gz(r-4.6-arm64)BayesSpace_1.23.0.tar.gz(r-4.6-x86_64)
BayesSpace_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BayesSpace/json (API)
| # 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:
On BioConductor:BayesSpace-1.23.0(bioc 3.24)BayesSpace-1.22.0(bioc 3.23)
softwareclusteringtranscriptomicsgeneexpressionsinglecellimmunooncologydataimportopenblascppopenmp
Last updated from:0411308424. Checks:1 NOTE, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 331 | ||
| linux-devel-arm64 | WARNING | 416 | ||
| linux-devel-x86_64 | WARNING | 500 | ||
| source / vignettes | OK | 481 | ||
| linux-release-arm64 | WARNING | 478 | ||
| linux-release-x86_64 | WARNING | 498 | ||
| macos-release-arm64 | WARNING | 261 | ||
| macos-release-x86_64 | WARNING | 627 | ||
| macos-oldrel-arm64 | WARNING | 328 | ||
| macos-oldrel-x86_64 | WARNING | 572 | ||
| windows-devel | WARNING | 789 | ||
| windows-release | WARNING | 798 | ||
| windows-oldrel | WARNING | 771 | ||
| wasm-release | OK | 291 |
Exports:adjustClusterLabelsclusterPlotcoreTunecounts2h5enhanceFeaturesexampleSCEfeaturePlotgetRDSmcmcChainparaLapplyqPlotqTuneread10Xh5readVisiumremoveChainspatialClusterspatialEnhancespatialPreprocess
Dependencies:abindarrowaskpassassertthatassortheadbase64encbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocNeighborsBiocParallelBiocSingularbitbit64bitopsblobblustercachemCairocliclustercodacodetoolscpp11curldata.tableDBIdbplyrDelayedArraydigestdir.expiryDirichletRegdplyrdqrngedgeRfarverfastmapfilelockFNNformatRFormulafutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttr2igraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmaxLikmclustmemoisemetapodmicrobenchmarkmiscToolsopensslpheatmappillarpkgconfigpngpurrrR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppDistRcppEigenRcppMLRcppProgressRCurlrhdf5rhdf5filtersRhdf5librjsonrlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorsS7sandwichScaledMatrixscalesscaterscranscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectutf8uwotvctrsviporviridisviridisLitewithrxgboostXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot spatial cluster assignments. | clusterPlot |
| Predict feature vectors from enhanced PCs. | enhanceFeatures |
| Create minimal 'SingleCellExperiment' for documentation examples. | exampleSCE |
| Plot spatial gene expression. | featurePlot |
| Download a processed sample from our S3 bucket | getRDS |
| Read MCMC chain associated with a BayesSpace clustering or enhancement | mcmcChain removeChain |
| Parallelization | paraLapply parallelize |
| Tuning the choice of q (number of clusters) before running spatialCluster | qPlot qTune |
| Load a Visium spatial dataset as a SingleCellExperiment. | counts2h5 read10Xh5 readVisium |
| Spatial clustering | spatialCluster |
| Enhance spot resolution | adjustClusterLabels coreTune spatialEnhance |
| Preprocess a spatial dataset for BayesSpace | spatialPreprocess |
