Package: BayesSpace 1.17.0
Matt Stone
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_1.17.0.tar.gz
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BayesSpace.pdf |BayesSpace.html✨
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
On BioConductor:BayesSpace-1.17.0(bioc 3.21)BayesSpace-1.16.0(bioc 3.20)
softwareclusteringtranscriptomicsgeneexpressionsinglecellimmunooncologydataimportopenblascppopenmp
Last updated 2 months agofrom:30b68f9156. Checks:OK: 7 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-win-x86_64 | OK | Nov 29 2024 |
| R-4.4-mac-x86_64 | OK | Nov 29 2024 |
| R-4.4-mac-aarch64 | OK | Nov 29 2024 |
| R-4.3-win-x86_64 | OK | Nov 29 2024 |
| R-4.3-mac-x86_64 | OK | Nov 29 2024 |
| R-4.3-mac-aarch64 | OK | Nov 29 2024 |
Exports:adjustClusterLabelsclusterPlotcoreTunecounts2h5enhanceFeaturesexampleSCEfeaturePlotgetRDSmcmcChainparaLapplyqPlotqTuneread10Xh5readVisiumremoveChainspatialClusterspatialEnhancespatialPreprocess
Dependencies:abindarrowaskpassassertthatassortheadbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularbitbit64bitopsblobblustercachemCairocliclustercodacodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestDirichletRegdplyrdqrngedgeRfansifarverfastmapfilelockFNNformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmaxLikmclustmemoisemetapodmgcvmicrobenchmarkmimemiscToolsmunsellnlmeopensslpheatmappillarpkgconfigplogrpngpurrrR6raggRColorBrewerRcppRcppAnnoyRcppArmadilloRcppDistRcppEigenRcppMLRcppProgressRCurlrhdf5rhdf5filtersRhdf5librjsonrlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorssandwichScaledMatrixscalesscaterscranscuttleSingleCellExperimentsitmosnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxgboostXVectorzlibbioczoo
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 |