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# BayesSpace <img src="inst/logo/logo.png" align="right" width="115" /> <!-- badges: start --> [![Bioconductor build status](]( <!-- badges: end --> ## Overview BayesSpace provides 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. ## System requirements ### Operating system BayesSpace has been built and tested on the following operating systems: * Linux: Ubuntu 18.04.4 LTS (Bionic Beaver) * macOS: 10.14.6 (Mojave), 10.15.6 (Catalina) * Windows: 10, Server 2012 R2 Standard ### Software dependencies BayesSpace requires R 4.0+ and Bioconductor 3.12+. Specific package dependencies are defined in the package DESCRIPTION and are managed by the Bioconductor and devtools installers. ## Installation BayesSpace is available through [Bioconductor]( ``` # Install the Bioconductor package manager, if necessary if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BayesSpace") ``` The development version can be installed via Bioconductor (see [instructions on using the devel branch]( or from github with `devtools`. ``` # Install devtools, if necessary if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("edward130603/BayesSpace") ``` Installation, including compilation, should take no more than one minute. ### Installing from source on macOS Installing from source on macOS (such as when installing via `devtools::install_github()`) requires [Fortran]( to compile the Rcpp code. Download links for the appropriate macOS versions can be found here: * Mojave (10.14) and Catalina (10.15) - [gfortran8.2]( * Sierra (10.12) and High Sierra (10.13) - [gfortran6.3]( Additional details on installing the R compiler tools for Rcpp on macOS can be found [in this blog post]( Note about homebrew: While gfortran is available via homebrew, we've encountered issues linking to its libraries after installation. We recommend installing directly from the [GNU Fortran repo]( ## Demonstration For an example of typical BayesSpace usage, please see our [package vignette]( for a demonstration and overview of the functions included in BayesSpace. Running the entire vignette takes approximately 5m30s on a Macbook Pro with a 2.0 GHz quad-core processor and 16 GB of RAM.