{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, and is fiscally sponsored by the Chan Zuckerberg Initiative.

• 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

You can install the development version of {anndataR} like so:

# 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:
  install.packages("hdf5r")
• To convert to/from SingleCellExperiment objects, install SingleCellExperiment:
  BiocManager::install("SingleCellExperiment")
• To convert to/from Seurat objects, install SeuratObject:
  install.packages("SeuratObject")

Alternatively, you can install all suggested dependencies at once:

pak::pak("scverse/anndataR", dependencies = TRUE)

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")
• Design: An overview of the design of the package.
  vignette("design", package = "anndataR")