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Create h5ad Specifications

Process Details

  • Name: Create h5ad
  • Process UUID: YzRvrM9h2R9nww6mvUytblLp7CMSKe
  • Process Group: SingleCell

Overview

This process converts a Seurat object stored in RDS format to an h5ad file format, enabling interoperability between R-based Seurat workflows and Python-based single-cell analysis tools like Scanpy. The conversion maintains the single-cell RNA sequencing data structure while ensuring compatibility across different analytical environments.

This process is implemented in R, utilizing the Seurat and SeuratDisk packages for data conversion.

Key Functionality

  • Format Conversion: Converts Seurat objects from RDS format to h5ad format for cross-platform compatibility
  • Metadata Processing: Handles factor-to-character conversion in metadata to ensure proper data type compatibility
  • Intermediate File Management: Creates temporary h5Seurat files as an intermediate step in the conversion process

Input/Output Specification

Inputs

Required Inputs

  • Seurat Object File
    • Description: A Seurat object containing single-cell RNA sequencing data, including expression matrices, metadata, and analysis results
    • Format: RDS

Outputs

  • h5ad File
    • Description: An AnnData-compatible h5ad file containing the converted single-cell data, suitable for use with Python-based analysis tools
    • Format: h5ad

Parameters & Settings

This process does not have user-configurable parameters.

References & Resources

  • Tool Documentation: Contact the team for details on the conversion script
  • Related Papers: Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018). Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology, 36(5), 411-420. https://doi.org/10.1038/nbt.4096