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 1.22.0
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_1.22.0.tar.gz
BayesSpace_1.22.0.zip(r-4.7-x86_64)BayesSpace_1.22.0.zip(r-4.7-arm64)BayesSpace_1.22.0.zip(r-4.6-x86_64)BayesSpace_1.22.0.zip(r-4.6-arm64)BayesSpace_1.22.0.zip(r-4.5-x86_64)
BayesSpace_1.22.0.tgz(r-4.6-x86_64)BayesSpace_1.22.0.tgz(r-4.6-arm64)BayesSpace_1.22.0.tgz(r-4.5-x86_64)BayesSpace_1.22.0.tgz(r-4.5-arm64)
BayesSpace_1.22.0.tar.gz(r-4.7-arm64)BayesSpace_1.22.0.tar.gz(r-4.7-x86_64)BayesSpace_1.22.0.tar.gz(r-4.6-arm64)BayesSpace_1.22.0.tar.gz(r-4.6-x86_64)
BayesSpace_1.22.0.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-release.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:dedd941a90 (on RELEASE_3_23). Checks:1 NOTE, 13 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 246 | ||
| linux-devel-arm64 | WARNING | 379 | ||
| linux-devel-x86_64 | WARNING | 593 | ||
| source / vignettes | OK | 492 | ||
| linux-release-arm64 | WARNING | 371 | ||
| linux-release-x86_64 | WARNING | 548 | ||
| macos-release-arm64 | WARNING | 262 | ||
| macos-release-x86_64 | WARNING | 813 | ||
| macos-oldrel-arm64 | WARNING | 294 | ||
| macos-oldrel-x86_64 | WARNING | 626 | ||
| windows-devel-arm64 | WARNING | 532 | ||
| windows-devel-x86_64 | WARNING | 661 | ||
| windows-release-arm64 | WARNING | 471 | ||
| windows-release-x86_64 | WARNING | 665 | ||
| windows-oldrel-x86_64 | WARNING | 735 | ||
| wasm-release | OK | 284 |
Exports:adjustClusterLabelsclusterPlotcoreTunecounts2h5enhanceFeaturesexampleSCEfeaturePlotgetRDSmcmcChainparaLapplyqPlotqTuneread10Xh5readVisiumremoveChainspatialClusterspatialEnhancespatialPreprocess
Dependencies:abindarrowaskpassassertthatassortheadbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocNeighborsBiocParallelBiocSingularbitbit64bitopsblobblustercachemcliclustercodacodetoolscpp11curldata.tableDBIdbplyrDelayedArraydigestdir.expiryDirichletRegdplyrdqrngedgeRfarverfastmapfilelockFNNformatRFormulafutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrepelgluegridExtragtablehttr2igraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmaxLikmclustmemoisemetapodmicrobenchmarkmiscToolsopensslpheatmappillarpkgconfigpurrrR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppDistRcppEigenRcppMLRcppProgressRCurlrhdf5rhdf5filtersRhdf5librjsonrlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorsS7sandwichScaledMatrixscalesscaterscranscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8uwotvctrsviporviridisviridisLitewithrxgboostXVectorzoo
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 |
