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# MuData [![R-CMD-check](]( [![pkgdown](]( [Documentation]( | [Preprint]( | [Discord]( `MuData` is a package that provides I/O funcitonality for `.h5mu` files and [MultiAssayExperiment]( objects. You can learn more about multimodal data containers in the reference [`mudata` documentation]( ## Installation `MuData` uses [`rhdf5`]( to access `.h5mu` and `.h5ad` files. In the meantime, the bioc-devel version of `rhdf5` must be used. `rhdf5` and `MuData` can be installed by running ```R remotes::install_github("grimbough/rhdf5") remotes::install_github("pmbio/MuDataMAE") ``` We use `rhdf5` over `hdf5r` to stay compatible with the rest of the Bioconductor ecosystem. In particular, using `hdf5r` would make integrating with other packages building on `rhdf5`, such as `HDF5Array`, much more difficult, if not impossible. We have implemented necessary HDF5 features that the `.h5ad` and consequently `.h5mu` formats make use of upstream, including [file creation properties]( and [object references]( ## Quick start `MuData` provides a set of I/O operations for multimodal data. `MuData` implements `WriteH5MU()` that saves MultiAssayExperiment objects to `.h5mu` files that can be further integrated into workflows in multiple programming languages, including the [`muon` Python library]( and the [`Muon.jl` Julia library]( `ReadH5MU()` reads `.h5mu` files into MultiAssayExperiment objects. ### Writing files Start with an existing dataset, e.g. a [MultiAssayExperiment]( object with five distinct modalities: ```R library(MultiAssayExperiment) data(miniACC) ``` `WriteH5MU()` allows to save the object into a `.h5mu` file: ```R library(MuData) WriteH5MU(miniACC, "miniACC.h5mu") ``` ### Reading files ```R miniACC <- ReadH5MU("miniACC.h5mu") ``` ## Relevant projects Other R packages for multimodal I/O include: - [MuDataSeurat]( for [Seurat]( objects - [SeuratDisk](