| MuData | AnnData [9, 17] | Seurat [8] | MultiAssay Experiment [14] | |
|---|---|---|---|---|
| Main programming environment | Python | Python | R | R |
| Objects can contain data out of memory (on disk) | Yes | Yes | No† | Yes‡ |
| Native serialisation accessible from multiple languages | Yes (.h5mu) | Yes (.h5ad) | No (.rds)†† | No (.rds)‡‡ |
| Native support for I/O operations | Python, Julia, R* | Python | R | R |
| Support for multiple modalities | Yes | No | Yes | Yes |
| Support for data missing in some modalities | Yes | NA | No | Yes |
| Support for multimodal embeddings | Yes | NA | No | No |
*Deserialized to MAE or Seurat objects
†With SeuratDisk library, in-memory Seurat objects can be constructed from parts of the data stored in HDF5 files
‡Only possible with HDF5Array library for matrices stored in external HDF5 files
††With SeuratDisk library, in-memory Seurat objects can be exported to HDF5 files
‡‡Only matrices stored in external HDF5 files, exported with HDF5Array library, can be accessed