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  • Install
  • Guide
  • Tutorials
  • Reference
  • GitHub

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  • 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 (FBA)
    • Multi-condition sparse FBA
    • Context-specific models (iMAT)
    • Multi-condition iMAT
  • Signaling
    • CARNIVAL
    • Multi-sample CARNIVAL
    • Acyclic boolean models of cell signaling (experimental)
  • 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
    • 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
    • Creating a new dataset from a dictionary
    • Querying features
    • Working across multiple samples
    • Saving and loading datasets
  • Plotting
    • Using graphviz
    • Using Pydot
    • Using NetworkX with Pydot
  • Constrained Optimization
    • The Knapsack Problem

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