Package: BayesSpace 1.15.0

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

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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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

On BioConductor:BayesSpace-1.15.0(bioc 3.20)BayesSpace-1.14.0(bioc 3.19)

bioconductor-package

13 exports 1.00 score 145 dependencies 1 dependents

Last updated 2 months agofrom:251a88c0d9

Exports:clusterPlot enhanceFeatures exampleSCE featurePlot getRDS mcmcChain qPlot qTune readVisium removeChain spatialCluster spatialEnhance spatialPreprocess

Dependencies:abind askpass assertthat beachmat beeswarm BH Biobase BiocFileCache BiocGenerics BiocNeighbors BiocParallel BiocSingular bit bit64 bitops blob bluster cachem Cairo cli cluster coda codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest DirichletReg dplyr dqrng edgeR fansi farver fastmap filelock FNN formatR Formula futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggplot2 ggrastr ggrepel glue gridExtra gtable httr igraph IRanges irlba isoband jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats maxLik mclust memoise metapod mgcv mime miscTools munsell nlme openssl pheatmap pillar pkgconfig plogr png purrr R6 ragg RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppDist RcppEigen RcppHNSW RcppML RcppProgress RCurl rhdf5 rhdf5filters Rhdf5lib rlang RSpectra RSQLite rsvd Rtsne S4Arrays S4Vectors sandwich ScaledMatrix scales scater scran scuttle SingleCellExperiment sitmo snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidyr tidyselect UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr xgboost XVector zlibbioc zoo

BayesSpace

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

Rendered fromBayesSpace.Rmdusingknitr::rmarkdownon Jun 26 2024.

Last update: 2021-11-04
Started: 2020-07-07

Citation

Development and contributors

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
Tuning the choice of q (number of clusters) before running spatialCluster	qPlot qTune
Load a Visium spatial dataset as a SingleCellExperiment.	readVisium
Spatial clustering	spatialCluster
Enhance spot resolution	spatialEnhance
Preprocess a spatial dataset for BayesSpace	spatialPreprocess