# {anndataR}: An R package for working with AnnData objects <img src="man/figures/logo.png" align="right" alt="anndataR logo" width=120 /> <!-- badges: start --> [](https://lifecycle.r-lib.org/articles/stages.html#stable) [](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check-bioc.yaml) [](https://app.codecov.io/gh/scverse/anndataR) [](https://bioconductor.org/checkResults/release/bioc-LATEST/anndataR) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/anndataR) [](http://bioconductor.org/packages/stats/bioc/anndataR/) [](https://support.bioconductor.org/tag/anndataR) [](https://bioconductor.org/packages/release/bioc/html/anndataR.html#since) [](http://bioconductor.org/checkResults/devel/bioc-LATEST/anndataR/) [](https://bioconductor.org/packages/release/bioc/html/anndataR.html#since) <!-- badges: end --> **{anndataR}** aims to make the `AnnData` format a first-class citizen in the R ecosystem, and to make it easy to work with AnnData files in R, either directly or by converting them to a `SingleCellExperiment` or `Seurat` object. **{anndataR}** is a an scverse® community project fiscally sponsored by the [Chan Zuckerberg Initiative](https://chanzuckerberg.com/). ## Features of {anndataR} - Provide an `R6` class to work with `AnnData` objects in R (either in-memory or on-disk) - Read/write `*.h5ad` files natively - Convert to/from `SingleCellExperiment` objects - Convert to/from `Seurat` objects Please [report](https://github.com/scverse/anndataR/issues) any issues you encounter. ## Installation You can install **{anndataR}** from Bioconductor using **BiocManager**: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("anndataR") ``` Or you can install the development version of **{anndataR}** from GitHub like so: ``` r # install.packages("pak") pak::pak("scverse/anndataR") ``` You will need to install additional dependencies, depending on the task you want to perform. - To read/write `*.h5ad` files, install [rhdf5](https://www.bioconductor.org/packages/rhdf5): `BiocManager::install("rhdf5")` - To convert to/from `SingleCellExperiment` objects, install [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html): `BiocManager::install("SingleCellExperiment")` - To convert to/from `Seurat` objects, install [SeuratObject](https://cran.r-project.org/package=SeuratObject): `install.packages("SeuratObject")` Alternatively, you can install all suggested dependencies at once: ``` r pak::pak("scverse/anndataR", dependencies = TRUE) ``` ## Getting started The best way to get started with **{anndataR}** is to explore the package vignettes (available at https://anndataR.scverse.org/articles/). In order to browse these vignettes locally, you need to build them during installation: ``` r options(pkg.build_vignettes = TRUE) pak::pak("scverse/anndataR") ``` Take note that you need all suggested dependencies available, and that building them can take some time. - [**Getting started**](https://anndataR.scverse.org/articles/anndataR.html): An introduction to the package and its features. `vignette("anndataR", package = "anndataR")` - [**Read/write `Seurat` objects**](https://anndataR.scverse.org/articles/usage_seurat.html): How to convert between `AnnData` and `Seurat` objects. `vignette("usage_seurat", package = "anndataR")` - [**Read/write `SingleCellExperiment` objects**](https://anndataR.scverse.org/articles/usage_singlecellexperiment.html): How to convert between `AnnData` and `SingleCellExperiment` objects `vignette("usage_singlecellexperiment", package = "anndataR")` - [**Software Design**](https://anndataR.scverse.org/articles/software_design.html): An overview of the design of the package - [**Development Status**](https://anndataR.scverse.org/articles/development_status.html): An overview of the development status of the package ## Citing **{anndataR}** If you use **{anndataR}** in your work, please cite [_"anndataR improves interoperability between R and Python in single-cell transcriptomics"_](https://doi.org/10.1101/2025.08.18.669052): ```r citation("anndataR") ``` Deconinck L, Zappia L, Cannoodt R, Morgan M, scverse core, Virshup I, Sang-aram C, Bredikhin D, Seurinck R, Saeys Y (2025). “anndataR improves interoperability between R and Python in single-cell transcriptomics.” _bioRxiv_, 2025.08.18.669052. doi:10.1101/2025.08.18.669052 <https://doi.org/10.1101/2025.08.18.669052>. A BibTeX entry for LaTeX users is @Article{, title = {{anndataR} improves interoperability between R and Python in single-cell transcriptomics}, author = {Louise Deconinck and Luke Zappia and Robrecht Cannoodt and Martin Morgan and {scverse core} and Isaac Virshup and Chananchida Sang-aram and Danila Bredikhin and Ruth Seurinck and Yvan Saeys}, journal = {bioRxiv}, year = {2025}, pages = {2025.08.18.669052}, doi = {10.1101/2025.08.18.669052}, }