scDesigner Demo: scATAC-seq PBMC Data in H5AD Format

scATAC-seq data from human peripheral blood mononuclear cells (PBMCs), processed into the H5AD format for use with the scanpy library. The dataset is 12.2 MB in size and was authored by Kris Sankaran. It was last updated on May 10, 2026.

Use Cases

• Benchmarking single-cell analysis pipelines based on scATAC-seq data.
• Demonstrating functionality for tools like scDesign3 that generate realistic synthetic data.
• Testing data loading and preprocessing workflows for the H5AD file format.
• Developing methods for multimodal single-cell and spatial omics integration.

Strengths

• Data is provided in the standardized H5AD format (12.2 MB), facilitating compatibility with popular analysis libraries like scanpy.
• Has a clear, permissive license (CC-BY-4.0) for open use and redistribution.
• Serves as a direct example dataset for the published method scDesign3.

Limitations

• Row and column counts are unknown, which limits assessment of the dataset's scale and feature richness.
• Column-level documentation is absent; field semantics must be inferred after download.
• Description metadata is limited; actual data quality requires manual inspection after download.

Provenance

Source

figshare

Collection Method

Processed scATAC-seq data from PBMCs, as investigated in the scDesign3 publication.

Freshness

Last updated 2026-05-10 20:17:49; freshness should be verified.