R quick start

Installation

TileDB-SOMA releases can be installed from R-universe, which serves macOS binaries and the source package for other Unix-like platforms.

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

Installing from source on Unix-like platforms requires cmake and git.

Alternatively, tiledbsoma can be installed directly from Conda, which serves binaries for multiple architectures.

mamba install -c conda-forge -c tiledb r-tiledbsoma

Note, we're using mamba here as a drop-in replacement for conda to accelerate the install process.

Version notes

As of October 2023 TileDB-SOMA-R 1.4.4 is released with a dependency on TileDB-R 0.20.3. Meanwhile TileDB-SOMA-R 1.5.0 is in prep and TileDB-R 0.21.1 exists. In order to obtain 0.20.3, you may use the following example which has been tested in a vanilla Docker image.

More generally:

• TileDB-SOMA 1.7 requires TileDB-R 0.23.0
• TileDB-SOMA 1.6 requires TileDB-R 0.22.0
• TileDB-SOMA 1.5 requires TileDB-R 0.21.3

docker run --rm -ti eddelbuettel/r2u:jammy

apt-get update
apt-get install -y cmake git ccache

Rscript -e 'install.packages("tiledbsoma", repos = c("https://tiledb-inc.r-universe.dev", "https://cloud.r-project.org"))'
Rscript -e 'update.packages(ask=FALSE)'
Rscript -e 'remotes::install_github(repo="TileDB-Inc/[email protected]")'
Rscript -e 'tiledbsoma::show_package_versions()'

Also please note the ccache caveat at https://github.com/single-cell-data/TileDB-SOMA/issues/1807.

R package documentation

https://single-cell-data.github.io/TileDB-SOMA/

Usage examples

Coming Soon