https://github.com/scverse/anndatar
AnnData interoperability in R
https://github.com/scverse/anndatar
anndata h5ad
Last synced: 11 months ago
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AnnData interoperability in R
- Host: GitHub
- URL: https://github.com/scverse/anndatar
- Owner: scverse
- License: other
- Created: 2023-04-26T15:26:39.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-07-06T12:59:37.000Z (11 months ago)
- Last Synced: 2025-07-06T13:46:12.444Z (11 months ago)
- Topics: anndata, h5ad
- Language: R
- Homepage: https://anndatar.data-intuitive.com
- Size: 1.41 MB
- Stars: 83
- Watchers: 10
- Forks: 12
- Open Issues: 25
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Funding: .github/FUNDING.yml
- License: LICENSE
Awesome Lists containing this project
README
# {anndataR}: An R package for working with AnnData objects 
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://CRAN.R-project.org/package=anndataR)
[](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check.yaml)
**{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 an scverse® community project maintained by [Data Intuitive](https://data-intuitive.com/), and is 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
> [!WARNING]
>
> This package is still in the experimental stage, and may not work as
> expected. You can find the status of development of anndataR on the
> [feature tracking page](https://anndatar.data-intuitive.com/articles/design.html#feature-tracking)
> of the website. Please [report](https://github.com/scverse/anndataR/issues) any issues you encounter.
## Installation
You can install the development version of **{anndataR}** 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 [hdf5r](https://cran.r-project.org/package=hdf5r):
`install.packages("hdf5r")`
- 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.data-intuitive.com/articles/).
- **Getting started**: An introduction to the package and its features.
`vignette("anndataR", package = "anndataR")`
- **Reading and writing H5AD files**: How to read and write `*.h5ad` files.
`vignette("usage_h5ad", package = "anndataR")`
- **Converting to/from Seurat objects**: How to convert between `AnnData` and `Seurat` objects.
`vignette("usage_seurat", package = "anndataR")`
- **Converting to/from SingleCellExperiment objects**: How to convert between `AnnData` and `SingleCellExperiment` objects.
`vignette("usage_singlecellexperiment", package = "anndataR")`
- **Software Design**: An overview of the design of the package.
`vignette("software_design", package = "anndataR")`
- **Development Status**: An overview of the development status of the package.
`vignette("development_status", package = "anndataR")`
- **Known Isses**: An overview of known issues with the package.
`vignette("known_issues", package = "anndataR")`