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@xueweic xueweic commented Oct 30, 2025

# Modifications from the original script:
# 1. Converted command-line interface (argparse) to function parameters for direct Python calling
# 2. Encapsulated the main script logic into a callable function
# 3. Made all parameters explicit function arguments with appropriate defaults
# 4. Preserved all core processing logic and algorithms from the original implementation
# 5. Supports three normalization methods:
#    - TMM + CPM with voom transformation (tmm_cpm_voom) [default]
#    - TMM + CPM with edgeR (tmm_cpm_edger)
#    - Quantile normalization (qn)
# 6. Added optional inverse normal transformation via the 'qnorm' parameter:
#    - 'qnorm': Apply inverse normal transformation after primary normalization
#    - 'none': Skip inverse normal transformation [default]

    # Modifications from the original script:
    # 1. Converted command-line interface (argparse) to function parameters for direct Python calling
    # 2. Encapsulated the main script logic into a callable function
    # 3. Made all parameters explicit function arguments with appropriate defaults
    # 4. Preserved all core processing logic and algorithms from the original implementation
    # 5. Supports three normalization methods:
    #    - TMM + CPM with voom transformation (tmm_cpm_voom) [default]
    #    - TMM + CPM with edgeR (tmm_cpm_edger)
    #    - Quantile normalization (qn)
    # 6. Added optional inverse normal transformation via the 'qnorm' parameter:
    #    - 'qnorm': Apply inverse normal transformation after primary normalization
    #    - 'none': Skip inverse normal transformation [default]
@gaow gaow merged commit b522676 into StatFunGen:main Oct 30, 2025
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2 participants