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Graphein 1.7.8
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Graphein 1.7.8

Getting Started

  • Installation
  • Graphein
  • Usage
  • License

Tutorials

  • Protein
    • Graphein - Residue Graph Tutorial
    • Graphein - Atom Graph Tutorial
    • Constructing Graphs from AlphaFold Protein Structure Database
    • Secondary Structure Graphs & Chain Graphs
    • Constructing Subgraphs in Graphein
    • Creating Protein Meshes in Graphein & 3D Visualisation
    • Protein Graph Analytics
    • Interactive Visualisation with Plotly
  • Molecules
    • Creating Molecular Graphs in Graphein
    • Working with Molecules from ZINC and ChEMBL
  • RNA Graphs
    • Graphein RNA Graph Construction Tutorial
    • Constructing 2D RNA Graphs
    • Constructing 3D Graphs of RNA Structures
    • Extracting Subgraphs from 3D RNA Structure Graphs
  • PPI Networks
    • PPI Networks and Structural Interactomics
  • Gene Regulatory Networks
    • Gene Regulatory Network Tutorial

Machine Learning

  • Protein Tensors
    • Working with Protein Tensors in Graphein
    • Datasets and DataLoaders
  • Datasets
    • Graphein Protein Structure Dataloaders
    • Learning at Proteome Scale!
    • Selection
    • Creating Datasets from the PDB
    • Making Selections
    • I/O
    • PSCDB - Protein Structural Change Database
    • PSCDB - Baselines
    • PPISP - Protein Protein Interaction Structure Prediction
  • Examples
    • Antibody Developability Prediction with E(N) GNNs
    • Predicting Acute Toxicity LD50
    • Splitting a Protein Dataset into Training and Test Sets

API Reference

  • graphein.protein
  • graphein.protein.tensor
  • graphein.molecule
  • graphein.rna
  • graphein.ppi
  • graphein.grn
  • graphein.ml
  • graphein.utils

Contributing

  • Introduction
  • Contributor guidelines
  • Your first contribution
  • Getting started
  • How to report a bug
  • How to suggest a feature or enhancement
  • How add a recommended VSCode Plugin
  • In closing
  • Contributor Covenant Code of Conduct
  • Contributors
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Gene Regulatory NetworksΒΆ

  • Gene Regulatory Network Tutorial
    • Config Objects
    • Gene List
    • Edge Annotation Functions
    • Graph Construction
    • Plotting the Graph
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Gene Regulatory Network Tutorial
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PPI Networks and Structural Interactomics
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