votti/mudata

MuData-compatible storage for bioconductor's MultiAssayExperiment

MuData

Documentation | Preprint | Discord

MuData is a package that provides I/O functionality 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

remotes::install_github("grimbough/rhdf5")
remotes::install_github("ilia-kats/MuData")

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:

library(MultiAssayExperiment)
data(miniACC)

WriteH5MU() allows to save the object into a .h5mu file:

library(MuData)
WriteH5MU(miniACC, "miniACC.h5mu")

Reading files

miniACC <- ReadH5MU("miniACC.h5mu")

Relevant projects

Other R packages for multimodal I/O include:

• MuDataSeurat for Seurat objects
• SeuratDisk