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README.md
# BayesSpace <img src="inst/logo/logo.png" align="right" width="115" /> <!-- badges: start --> [![Bioconductor build status](http://bioconductor.org/shields/build/release/bioc/BayesSpace.svg)](https://bioconductor.org/checkResults/3.14/bioc-LATEST/BayesSpace/) <!-- 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](https://bioconductor.org/packages/3.12/bioc/html/BayesSpace.html). ``` # 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](https://www.bioconductor.org/developers/how-to/useDevel/)) 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](https://github.com/fxcoudert/gfortran-for-macOS) 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](https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg) * Sierra (10.12) and High Sierra (10.13) - [gfortran6.3](https://github.com/fxcoudert/gfortran-for-macOS/releases/download/6.3/gfortran-6.3-Sierra.dmg) Additional details on installing the R compiler tools for Rcpp on macOS can be found [in this blog post](https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/). 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](https://github.com/fxcoudert/gfortran-for-macOS). ## Demonstration For an example of typical BayesSpace usage, please see our [package vignette](https://edward130603.github.io/BayesSpace/articles/BayesSpace.html) 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.