Overview

This is a R implementation of the Unified Single-cell Data Model.

This branch, main, implements the updated specfication. Please also see the main-old branch which implements the original specification.

Installation

Using R-universe

This code is hosted at R-universe, so you can do

$ install.packages('tiledbsoma', repos = c('https://tiledb-inc.r-universe.dev', 'https://cloud.r-project.org'))

From source

Requirements

• Source installation requires the tiledb R package (which in turn depends on the tiledb Core library).
• In general, source installation of TileDB and its packages may require cmake and git to be installed; these are common tools each operating system provides readily.
• Other R package dependencies are listed in the DESCRIPTION file and can be installed via e.g. remotes::install_deps(".", TRUE). In order to build vignettes, knitr and rmarkdown are required as is testthat for testing. If testthat is invoked directly then pkgbuild is also needed.
• In addition, the R package also depends on the libtiledbsoma library -- which gets installed with the package as described in the next section.

Step-by-step

• Clone this repository: git clone https://github.com/single-cell-data/TileDB-SOMA.git
• Change into the R API package directory: cd TileDB-SOMA/apis/r
• Optionally, clean the files in the repo: ./cleanup (this is not needed the first time)
• Access to more test data: install.packages("pbmc3k.tiledb", repos="https://ghrr.github.io/drat") `
• Optionally, update the libtiledbsoma sources: ./copy_source.sh (which updates the includes tarball of libtiledbsoma).
• If you have edited any src/*.cpp with RcppExport then run Rscript -e 'Rcpp::compileAttributes()'
• Build the R package source tarball from the repository sources: R CMD build . (which will also build libtiledbsoma from source; other dependencies are required as described in the previous section)
• If you have changed any signatures, run Rscript -e 'roxygen2::roxygenise()'
• Check and test the package from the tarball: R CMD check --no-vignettes --no-manual tiledbsoma_*.tar.gz
  • For quicker iteration, run Rscript -e 'testthat::test_local("tests/testthat")'
• Install the package from the tarball: R CMD INSTALL tiledbsoma_*.tar.gz

Once installed successfully, the package sources can be edited and re-installed. The optional clean step ensures a full rebuild, and the optional copy of libtiledbsoma ensures it is updated too.

Status

Please see https://github.com/single-cell-data/TileDB-SOMA/issues.

Information for developers

Please see the TileDB-SOMA wiki.