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38 changes: 38 additions & 0 deletions docs/user-guide/supported-data/supported-data.md
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Expand Up @@ -163,6 +163,44 @@ in our **Advanced User Guide**.

## HDF5 (e.g. Single Cell)

!!! info "Limitations"
HDF5 is supported as Attached File in ODM with ability to observe and search by File Structure (Contents) only.
We are working on full functionality for HDF5 data content parsing, search, and filtering.

**HDF5 (Hierarchical Data Format version 5)** is a widely used data format in genomic research, particularly in
Single Cell studies. It is designed to store large, complex datasets efficiently, making it a preferred choice for
structured biological data such as gene expression matrices and metadata.

The ODM now supports HDF5 file upload as Attached File, search by File Structure (Contents), and manage these
files within Studies.

### Supported HDF5 Formats

- **.h5, .h5ad** - Standard HDF5 files
- **.h5.gz, .h5ad.zip** - Compressed versions of standard HDF5 files

### Viewing File Structure (Contents)

- **Access File Contents via GUI**: The ODM displays File Contents on the Data Tab of Metadata Editor. It is
accessible on `Contents` button click.
- **Retrieve File Contents via API**: You can retrieve File Contents for the list of files or by unique
Genestack Accession.

### Searching HDF5 Files by File Contents

Users can search via GUI and API for:

- **Unique File**: by Genestack Accession.
- **Files**:

- By File Contents fields/pathways.
- By Study Genestack Accession.

- **Studies**:

- By File Contents fields/pathways.
- By File Genestack Accession.

For a detailed description and instructions on using HDF5, visit the **[Supported Data Formats page](../doc-odm-user-guide/supported-formats.md)**
in our **Advanced User Guide**.

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