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BayesSpace
This is thereleased version of BayesSpace; for the devel version, seeBayesSpace.
Clustering and Resolution Enhancement of Spatial Transcriptomes
Bioconductor version: Release (3.22)
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.
Author: Edward Zhao [aut], Senbai Kang [aut, cre], Matt Stone [aut], Xing Ren [ctb], Raphael Gottardo [ctb]
Maintainer: Senbai Kang <senbai.kang at chuv.ch>
citation("BayesSpace")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("BayesSpace")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BayesSpace")| BayesSpace | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering,DataImport,GeneExpression,ImmunoOncology,SingleCell,Software,Transcriptomics |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| License | MIT + fileLICENSE |
| Depends | R (>= 4.0.0),SingleCellExperiment |
| Imports | Rcpp (>= 1.0.4.6), stats, methods,purrr,scater,scran,SummarizedExperiment,coda,rhdf5,S4Vectors,Matrix,magrittr,assertthat,arrow,mclust,RCurl,DirichletReg,xgboost (< 2.0.0), utils,dplyr,rlang,ggplot2,tibble,rjson,tidyr,scales,microbenchmark,BiocFileCache,BiocSingular,BiocParallel |
| System Requirements | C++17 |
| URL | edward130603.github.io/BayesSpace |
| Bug Reports | https://github.com/edward130603/BayesSpace/issues |
See More
| Suggests | testthat,knitr,rmarkdown,igraph,spatialLIBD,viridis,patchwork,RColorBrewer,Seurat |
| Linking To | Rcpp,RcppArmadillo,RcppDist,RcppProgress |
| Enhances | |
| Depends On Me | |
| Imports Me | RegionalST, OSTA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | BayesSpace_1.20.0.tar.gz |
| Windows Binary (x86_64) | BayesSpace_1.20.0.zip |
| macOS Binary (x86_64) | BayesSpace_1.20.0.tgz |
| macOS Binary (arm64) | BayesSpace_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BayesSpace |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BayesSpace |
| Bioc Package Browser | https://code.bioconductor.org/browse/BayesSpace/ |
| Package Short Url | https://bioconductor.org/packages/BayesSpace/ |
| Package Downloads Report | Download Stats |