ODAMNet documentation

ODAMNet is a set of three different approaches to study the molecular relationship between chemicals and rare diseases. These three approaches are Overlap analysis, diffusion analysis using random walk with restart and active module identification.

This project was created within the framework of the EJRP-RD project.

If you use ODAMNet, please cite our publication:

Térézol M, Baudot A, Ozisik O. ODAMNet: A Python package to identify molecular relationships between chemicals and rare diseases using overlap, active module and random walk approaches. SoftwareX. 2024;26:101701. doi: 10.1016/j.softx.2024.101701.

Quickstart

• Installation
• Usage

Approaches

• Overview of the approaches
  • Goal
  • References
• Overlap analysis
  • Principle
  • Usage
  • Input parameters for the Overlap analysis
  • Use-cases command lines
  • References
• Active Module Identification
  • Principle
  • Overview of the DOMINO algorithm
  • Usage
  • Input parameters for the AMI
  • Use-cases command lines
  • References
• Random Walk with Restart
  • Principle
  • Usage
  • Input parameters for the RWR
  • Use-cases command lines
  • References

Networks

• Network downloading
  • Principle
  • Input parameters for network downloading
  • Use-case command lines
  • References
• Network creation
  • Principle
  • Input parameters for network creation
  • Use-case command lines
  • References
• Network visualisation
  • Active module identification results visualisation
  • Random walk with restart results visualisation
  • References
• Networks used
  • Genes multilayer network
  • Pathways/processes of interest network
  • Disease-disease similarity network
  • References

Use-cases

• Use-case 1: data are retrieved automatically by queries
  • Overlap analysis
  • Active Module Identification (AMI)
  • Random Walk with Restart (RWR)
  • Overlap, AMI and RWR results comparison
  • References
• Use-case 2: data are provided by the user
  • Context
  • Overlap analysis
  • Active Module Identification (AMI)
  • Random Walk with Restart (RWR)
  • Overlap, AMI and RWR results comparison
  • References

File formats

• Input files
  • Target genes
  • Pathways/processes of interest
  • Networks
  • Configuration file
  • References
• Output files
  • Query output files
  • Overlap analysis output files
  • AMI output files
  • RWR output files
  • References

Code description

• Input parameters for each approach
• Code functions in details

Indices and tables

• Index

• Module Index

• Search Page