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  • Installation Guide
    • Installation requirements
    • Dependencies
    • Installation
  • User Guide
    • Prepare input data
      • The Allen Human Brain Atlas dataset
        • Arguments to zoom.prepare.abagen_ctx()
      • The spatial brain phenotype data
      • The single-cell RNA sequencing data
        • Arguments to zoom.sc_tool.compute_gss()
    • Imaging-transcriptomics
      • Construct main class of zoom
        • Arguments to zoom.core.ZOOM() and zoom.core.ZOOM_SC()
      • Partial least squares regression
        • Arguments to class method ZOOM_SC.cv_PLSR()
      • Gene contribution statistics
        • Arguments to class method ZOOM_SC.get_gene_contrib()
      • Pick optimally sized gene set
        • Arguments to class method ZOOM_SC.test_gene_size()
      • Spatial permutation-based GSEA
        • Arguments to class method ZOOM_SC.GSEA()
    • Single-cell enrichment score of SBP-relevant gene set
      • Single-cell scoring
        • Arguments to zoom.prepare.abagen_ctx()
      • Downstream analyses
        • Arguments to zoom.prepare.abagen_ctx()
  • What’s new
    • 0.0.1 (December 20, 2025)
  • API Documents
    • zoom.core - Core Class
      • zoom.core.ZOOM
        • ZOOM
      • zoom.core.ZOOM_SC
        • ZOOM_SC
    • zoom.data_loader - Data Loader
      • zoom.data_loader.load_sc
        • load_sc()
      • zoom.data_loader.load_gii
        • load_gii()
      • zoom.data_loader.load_parc
        • load_parc()
    • zoom.prepare - Prepare Input Data
      • zoom.prepare.abagen_ctx
        • abagen_ctx()
      • zoom.prepare.process_SBP
        • process_SBP()
      • zoom.prepare.fetch_medial_wall
        • fetch_medial_wall()
    • zoom.pls_tool - Imaging Transcriptomics
      • zoom.pls_tool.optimal_component_eval
        • optimal_component_eval()
      • zoom.pls_tool.run_component_eval
        • run_component_eval()
      • zoom.pls_tool.model_eval
        • model_eval()
      • zoom.pls_tool.pls_perm
        • pls_perm()
      • zoom.pls_tool.vip_perm
        • vip_perm()
      • zoom.pls_tool.boot_pls1
        • boot_pls1()
      • zoom.pls_tool.pls1_perm
        • pls1_perm()
    • zoom.sc_tool - Single Cell Scoring
      • zoom.sc_tool.preprocess
        • preprocess()
      • zoom.sc_tool.rank_expression
        • rank_expression()
      • zoom.sc_tool.compute_gss
        • compute_gss()
      • zoom.sc_tool.select_ctrl
        • select_ctrl()
      • zoom.sc_tool.score_cell_zoom
        • score_cell_zoom()
      • zoom.sc_tool.group_bh
        • group_bh()
      • zoom.sc_tool.downstream_DEG
        • downstream_DEG()
      • zoom.sc_tool.downstream_region_enrich
        • downstream_region_enrich()
      • zoom.sc_tool.gsea_perm
        • gsea_perm()
  • References
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