BayesSpace
Clustering and Resolution Enhancement of Spatial Transcriptomes
Bioconductor version: Release (3.20)
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], Matt Stone [aut, cre], Xing Ren [ctb], Raphael Gottardo [ctb]
Maintainer: Matt Stone <mstone at fredhutch.org>
citation("BayesSpace")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BayesSpace")
For older versions of R, please refer to the appropriate Bioconductor 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 | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | MIT + file LICENSE |
| 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, 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BayesSpace_1.16.0.tar.gz |
| Windows Binary (x86_64) | BayesSpace_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | BayesSpace_1.16.0.tgz |
| macOS Binary (arm64) | BayesSpace_1.15.3.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 |