rhdf5/Rhdf5lib

rhdf5 – HDF5 Data Access for R

rhdf5 and Rhdf5lib provide an interface between the HDF5 file format and R. HDF5 supports portable storage and access of very large or complex datasets together with rich metadata. The rhdf5 package enables R applications to exchange HDF5-based data with other software and to work with datasets that may exceed available memory. It is particularly important in single-cell data analysis, where HDF5-based formats are widely used to manage rapidly growing dataset sizes.

Key benefits
Provides HDF5 file access from R and Bioconductor workflows
Supports storage and exchange of large and complex datasets
Enables access to data that may be larger than available RAM
Handles structured data and metadata in a portable file format
Serves as infrastructure for many single-cell and large-scale omics tools
Applications
Reading and writing HDF5 files in R
Exchange of large datasets between R and other software environments
Management of complex omics and single-cell datasets
Development of scalable R/Bioconductor analysis workflows
Access to disk-based data structures for memory-efficient analysis
Intended use

rhdf5 is intended for bioinformaticians, computational biologists, single-cell researchers, R package developers, and data scientists who need reliable access to HDF5 files from R. It is particularly suited for workflows involving large or complex datasets, structured metadata, and interoperable data exchange between R and other analysis tools.

Contact:
Website https://github.com/Huber-group-EMBL/rhdf5/issues