revise-svc

Start Here

  • Concepts
    • What Is an SVC?
    • Route Selection
    • Confounding Factors
    • Inputs and Outputs
    • Where to Go Next
  • Quick Start
    • Install
    • Download Data
    • Run sp-SVC for hST
    • Run sc-SVC for iST
    • Run a Benchmark Case
    • Use the Python API
    • Validate a Development Checkout
    • Next Steps
  • Installation
    • Prerequisites
    • Stable Release
    • Development Install
    • Documentation Build
    • Data Layout

Run REVISE

  • Application mode
    • Choose an Application Route
    • sp-SVC Application
    • sc-SVC Application
    • Advanced Application Profiles
  • Benchmark mode
    • At a Glance
    • Supported Confounding Factors
    • Command-Line Usage
    • Python API
    • Benchmark Notebooks
      • segmentation benchmark
        • Plot seg benchmark
        • bin2cell
      • spot size benchmark
      • batch effect benchmark
        • HVG
        • All genes
      • imputation benchmark
  • Configuration
    • Mental Model
    • Resolution Order
    • Profiles
    • Router
    • Override Examples
    • Locked Parameters
    • Output Layout

Gallery

  • Application cases
    • Prepare Data
    • Application Case Notebooks
      • sp-SVC Visium HD
        • Notebook Guide
        • First glimpse at raw data
        • Spatial Autocorrelation
        • Prerequisites
        • Clustering metric
        • Input And Cache Checks
        • Plot summary ARI and NMI
        • Metric Comparison
        • Plot spatial correlation
        • Analysis CAF surrounded tumor in P1CRC
        • Dotplot analysis to visualize marker specificity
        • Marker Program Visualization
      • sc-SVC T cells
        • Notebook Guide
        • Load Reconstructed SVCs
        • Spatial Subtype Maps
        • bioinfo analysis
        • Marker And Differential Programs
      • sc-SVC Monocyte
        • Notebook Guide
        • Load Reconstructed SVCs
        • Spatial Subtype Maps
        • bioinfo analysis
        • Marker And Differential Programs
        • CCI
      • sc-SVC Fibroblast
        • Notebook Guide
        • Load Reconstructed SVCs
        • Spatial Subtype Maps
        • Marker gene analysis
        • Marker And Differential Programs
        • sc_SVC subclusters bioinformatical analysis
        • sc-SVC subtypes analysis
        • Pseudotime analysis
      • sc-SVC Visium mouse brain
        • Notebook Guide
        • Case Design And Assumptions
        • 1. Configure Paths
        • 2. Fetch The Input Files
        • 3. Load Data And Audit Contents
        • 4. Build REVISE-Ready Input Objects
        • 5. Allocate Virtual Cells From Transcript Abundance
        • 6. Save Prepared Inputs And The Virtual-Cell Prior
        • 7. Run REVISE Reconstruction
        • 8. Inspect The Reconstructed SVC Object
        • 9. Spatial Layout Of Reconstructed Cell Types
        • 10. Representative Reconstructed Gene Maps
        • 11. Expression-Space Overview
        • 12. Output Checklist

Reference

  • Architecture
    • System Map
    • Public Entry Point
    • Configuration Surface
    • Unified Lifecycle
    • Registries and Plugins
    • Run Artifacts
    • Extension Checklist
  • API
    • Pipeline
      • revise.framework.REVISEPipeline
        • REVISEPipeline
      • revise.recon.context.PipelineContext
        • PipelineContext
      • revise.recon.pipeline.UnifiedReconstructionPipeline
        • UnifiedReconstructionPipeline
      • revise.svc.SVC
        • SVC
    • Facade Helpers
      • revise.recon.facade.sp_svc
        • sp_svc()
      • revise.recon.facade.sc_svc
        • sc_svc()
    • Configuration
      • revise.config.runner_conf.ApplicationSpConf
        • ApplicationSpConf
      • revise.config.runner_conf.ApplicationScConf
        • ApplicationScConf
      • revise.config.runner_conf.ApplicationScSrConf
        • ApplicationScSrConf
      • revise.config.runner_conf.BenchmarkSrConf
        • BenchmarkSrConf
      • revise.config.runner_conf.BenchmarkSegConf
        • BenchmarkSegConf
      • revise.config.runner_conf.BenchmarkImputeConf
        • BenchmarkImputeConf
    • Analysis Services
      • revise.analysis.ScSVCAnalysisService
        • ScSVCAnalysisService
      • revise.analysis.SpSVCAnalysisService
        • SpSVCAnalysisService
      • revise.analysis.compute_metric
        • compute_metric()
      • revise.analysis.compute_clustering_metrics
        • compute_clustering_metrics()
    • Registries and Plugins
      • revise.backend.registry.StrategyRegistry
        • StrategyRegistry
      • revise.backend.registry.PluginRegistry
        • PluginRegistry
      • revise.backend.contracts.LocalRefinementStrategy
        • LocalRefinementStrategy
      • revise.backend.contracts.PlatformAdapter
        • PlatformAdapter
      • revise.backend.contracts.CFStrategy
        • CFStrategy
      • revise.backend.contracts.OTSolver
        • OTSolver
    • Backend Compatibility Runners
      • revise.backend.runners.sp_svc_application.SpSVC
        • SpSVC
      • revise.backend.runners.sc_svc_application.ScSVC
        • ScSVC
      • revise.backend.runners.sc_svc_sr_application.ScSVCSr
        • ScSVCSr
      • revise.backend.runners.sp_svc_benchmark.SpSVC
        • SpSVC
      • revise.backend.runners.sc_svc_sr_benchmark.ScSVCSr
        • ScSVCSr
      • revise.backend.runners.sc_svc_impute_benchmark.ScSVCImpute
        • ScSVCImpute
revise-svc
  • Overview: module code

All modules for which code is available

  • revise.analysis.metrics
  • revise.analysis.services
  • revise.backend.contracts
  • revise.backend.registry
  • revise.backend.runners.sc_svc_application
  • revise.backend.runners.sc_svc_impute_benchmark
  • revise.backend.runners.sc_svc_sr_application
  • revise.backend.runners.sc_svc_sr_benchmark
  • revise.backend.runners.sp_svc_application
  • revise.backend.runners.sp_svc_benchmark
  • revise.config.runner_conf
  • revise.framework
  • revise.recon.context
  • revise.recon.facade
  • revise.recon.pipeline
  • revise.svc.model

© Copyright 2025-2026, Yushuai Wu and Yifeng Jiao.

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