immuneREF: Reference-based similarity comparison of immune repertoires

immuneREF allows the analysis of repertoire similarity on a one-to-one, one-to-many and many-to-many scale across repertoire features ranging from fully sequence- to fully frequency-dependent ones.

The immuneREF workflow combines the analysis of a range of features to calculate a multidimensional similarity network of immune repertoires. This enables the identifciation of both, global repertoire similarity (many-to-many, one-to-many) and similarity to a reference repertoires (many-to-one, one-to-one)

Contents:

• Installing immuneREF
  • Prerequisites
  • Install immuneREF
• Quickstart
  • Quickstart
• In-depth Tutorial
  • Overview
  • The workflow of the quickstart analysis
  • 1. Input format
  • 2. Analysis of single features
  • 3. Similarity score calculation
  • 4. Condensing layers into multi-layer network
  • 5. Visualization of results
  • 6. Flowchart immuneREF workflow
  • References
• immuneREF feature layers
  • The feature layers of immuneREF (Overview)
  • References
• Determining repertoire similarities
  • Similarity per feature
  • Table similarity calculation per feature
  • Similarity calculation for all features
  • References
• Multi-layer analysis
  • Condensing multiple layers
• Analysis of immuneREF output
  • Analyzing Similarity Networks
  • Bonus: Network characteristics
  • References
• Additional Exploratory Analysis
  • Gene expression exploratory analysis
  • References
• Acknowledgments

Indices and tables

• Index
• Module Index
• Search Page