BayesSpace
This is the released version of BayesSpace; for the devel version, see BayesSpace.
Clustering and Resolution Enhancement of Spatial Transcriptomes
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 (>= 3.0.0), 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
Follow Installation instructions to use this package in your R session.
| Source Package | BayesSpace_1.22.0.tar.gz |
| Windows Binary (x86_64) | BayesSpace_1.22.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BayesSpace_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | BayesSpace_1.22.0.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 |