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Prepare H5ad Specifications

Process Details

  • Name: prepare_h5ad
  • Process UUID: c6636355jnf84yunhpx39w57w1h480
  • Process Group: Cell Type Mapper

Overview

This process converts single-cell RNA sequencing data from R data structure (RDS) format to the standardized H5AD format used by Python-based single-cell analysis tools. The conversion enables seamless integration with cell type mapping workflows and other Python-based analytical pipelines in the scanpy ecosystem.

This process is implemented in Bash, which invokes an R script for data format conversion.

Key Functionality

  • Format Conversion: Converts RDS files containing single-cell data to H5AD format
  • Data Structure Preservation: Maintains cell metadata, gene expression matrices, and annotations during conversion
  • Pipeline Integration: Prepares data for downstream cell type mapping and classification workflows

Input/Output Specification

Inputs

Required Inputs

  • RDS File
    • Description: Single-cell RNA sequencing data stored in R data structure format, typically containing expression matrices and cell/gene metadata
    • Format: RDS

Outputs

  • H5AD File
    • Description: Single-cell data converted to H5AD format, compatible with Python-based analysis tools like scanpy and cell type mapping algorithms
    • Format: H5AD

Parameters & Settings

This process uses default conversion parameters and does not expose user-configurable settings in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on prepare_h5ad.R