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Create h5ad copy Specifications

Process Details

  • Name: Create_h5ad_copy
  • Process UUID: 71314e90c17347cc834648a640f8b69f
  • Process Group: SingleCell

Overview

This process converts Seurat objects (stored in RDS format) to h5ad format, enabling interoperability between R-based Seurat workflows and Python-based single-cell analysis tools like Scanpy. The conversion preserves cell metadata, gene expression data, and dimensional reductions while ensuring compatibility across different analysis platforms.

This process is implemented in R, which invokes a Python script for the final h5ad conversion using the h5seurat_to_h5ad_converter.py tool.

Key Functionality

  • Format Conversion: Converts Seurat objects from RDS format to h5ad format for cross-platform compatibility
  • Metadata Processing: Automatically converts factor columns to character format to ensure HDF5 export consistency
  • Seurat V5 Compatibility: Handles Seurat V5 objects with proper layer data preservation during conversion
  • Two-Stage Process: First converts to intermediate H5Seurat format, then to final h5ad format

Input/Output Specification

Inputs

Required Inputs

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

Outputs

  • h5ad File
    • Description: Single-cell data in h5ad format compatible with Python analysis tools like Scanpy, containing the same expression data and metadata as the input Seurat object
    • Format: h5ad

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on h5seurat_to_h5ad_converter.py
  • Related Papers: Stuart, T., Butler, A., Hoffman, P. et al. Comprehensive Integration of Single-Cell Data. Cell 177, 1888-1902.e21 (2019). https://doi.org/10.1016/j.cell.2019.05.031