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  • Install
  • Guide
  • Tutorials
  • Reference
  • Release Notes
  • GitHub

Section Navigation

  • Getting started
    • Prior Knowledge and Graphs
    • Working with data
    • Plotting
    • Constrained Optimization
  • Network methods
    • Shortest paths
    • Multi-sample shortest paths
    • Multi-commodity Network Flows
    • Acyclic Flows
    • Steiner trees
    • Prize-Collecting Steiner Trees (PCST)
    • Multi-sample PCST
  • Metabolism
    • Flux balance analysis
    • Multi-condition FBA
    • Integrating gene expression into metabolic models
    • Multi-condition gene expression integration
  • Signaling
    • CARNIVAL
    • Multi-sample CARNIVAL
    • PHONEMeS
    • Global upstream and downstream PHONEMeS
    • Inferring intracellular signaling models with CellNOptDAG
  • Interoperability
    • COBRApy: Constraint-based metabolic modeling in Python
    • LIANA+: An all-in-one cell-cell communication framework
    • Decoupler: Ensemble of methods to infer biological activities
    • Omnipath: intra- & intercellular signaling knowledge
    • NetworkX: Network Analysis in Python
    • AnnNet
    • CVXPY: Convex optimization, for everyone
    • PICOS: A Python interface to conic optimization solvers
  • Guide
  • Getting started

Getting started#

  • Prior Knowledge and Graphs
    • Manually creating a graph
    • Edge attributes
    • Modyfing attributes
    • Importing graphs
    • Saving and reading
    • Hypergraphs
  • Working with data
    • Samples and features
    • Creating a dataset
    • Querying measurements
    • Copying and extending data
    • Saving and loading data
    • Using data with methods
  • Plotting
    • 1. Basic graph visualization
    • 2. Visual encoding from values
      • Targeted per-element style overrides
    • 3. Presets for common workflows
      • Metabolic flux visualization
      • Method-aware presets and role styling
    • 4. Theme customization
    • 5. Export and interoperability
    • 6. Browser/WASM rendering
    • 7. Custom processors
  • Constrained Optimization
    • The Knapsack Problem

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