Interoperability

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Interoperability#

The on-disk representation of anndata files can be read from other languages. Here we list interfaces for working with AnnData from your language of choice:

R#

  • anndataR allows reading and writing AnnData objects stored in HDF5 and Zarr (v2 and v3) formats. Conversion functions to Seurat and SingleCellExperiment are also provided.

  • zellkonverter zellkonverter provides basilisk based tooling for loading from h5ad files to SingleCellExperiment

  • anndata for R provides an R implementation of AnnData as well as IO for the HDF5 format. Superseded by anndataR!

  • MuData provides IO for AnnData and MuData stored in HDF5 to Bioconductor’s SingleCellExperiment and MultiAssayExperiment objects.

  • MuDataSeurat provides IO from AnnData and MuData stored in HDF5 to Seurat objects.

Julia#

  • Muon.jl provides Julia implementations of AnnData and MuData objects, as well as IO for the HDF5 format

  • scVI.jl provides a Julia implementation of AnnData as well as IO for the HDF5 format.

Javascript#

  • Vitessce contains loaders from AnnDatas stored as Zarr, and uses this to provide interactive visualization

Rust#

  • anndata-rs provides a Rust implementation of AnnData as well as advanced IO support for the HDF5 storage format.

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