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Process Anndata Specifications

Process Details

  • Name: process_anndata
  • Process UUID: 6a032ec874034e28836ae3c8e5ddf455
  • Process Group: SingleCell

Overview

This process performs preprocessing and integration of single-cell RNA sequencing data by combining AnnData (h5ad) and Loom file formats. It is designed to prepare single-cell datasets for downstream velocity analysis and visualization workflows.

This process is implemented in Bash, which invokes a Python script for AnnData preprocessing and integration.

Key Functionality

  • Data Integration: Combines single-cell data from h5ad and loom file formats into a unified AnnData object
  • Preprocessing: Applies standard preprocessing steps to prepare data for velocity analysis
  • Format Standardization: Outputs a processed h5ad file compatible with scVelo and other single-cell analysis tools

Input/Output Specification

Inputs

Required Inputs

  • Loom File

    • Description: Loom format file containing single-cell RNA sequencing data with spliced and unspliced transcript counts
    • Format: .loom

  • H5AD File

    • Description: AnnData format file containing processed single-cell RNA sequencing data
    • Format: .h5ad

Outputs

  • Processed H5AD
    • Description: Integrated and preprocessed AnnData object ready for velocity analysis
    • Format: .h5ad

References & Resources

  • Tool Documentation: Contact the team for details on preprocess_anndata.py
  • Related Papers: Bergen, V., Lange, M., Peidli, S. et al. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol 38, 1408–1414 (2020). https://doi.org/10.1038/s41587-020-0591-3