Data

The current validated example workflow uses a mouse brain RNA + peak dataset.

Required input files

The current example expects three input files:

  • sc_mousebrain_processed.h5ad: single-cell reference RNA

  • RNA.h5ad: spatial RNA

  • peak.h5ad: spatial peak data

Example directory layout

A typical dataset layout is:

<data_root>/mousebrain_H3K27ac/
├── sc_mousebrain_processed.h5ad
├── RNA.h5ad
└── peak.h5ad

How to obtain the data

The example dataset is not currently distributed through a public download link.

To obtain the validated example files, please contact the maintainer.

How to prepare data

After obtaining the required files, place them into a local data directory matching the expected structure.

The file paths can then be configured in the pipeline configuration.

Example

After preparing the dataset, the input directory may look like:

data/
└── mousebrain_H3K27ac/
   ├── sc_mousebrain_processed.h5ad
   ├── RNA.h5ad
   └── peak.h5ad

Notes

  • The current validated workflow uses single-cell reference RNA, spatial RNA, and a second spatial modality.

  • The main tutorial currently follows the validated mouse brain example.

  • Public dataset download links or automated download scripts may be added in future releases.