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Tutorials

Welcome to the LZGraphs tutorials. These step-by-step guides will help you master TCR repertoire analysis using LZGraphs.

Learning Path

We recommend following these tutorials in order:

1. Graph Construction

Beginner · 15 minutes

Learn to build AAP, NDP, and Naive graph variants from your data.

2. Sequence Analysis

Beginner · 20 minutes

Calculate sequence probabilities, explore graph structure, and simulate new sequences.

3. Diversity Metrics

Intermediate · 15 minutes

Measure repertoire complexity using k-diversity, Hill numbers, and occupancy models.

Prerequisites

Before starting, ensure you have:

Sample Data

All tutorials use example data included with LZGraphs:

import csv

# Load sample data
with open("examples/ExampleData1.csv") as f:
    sequences = [row['cdr3_amino_acid'] for row in csv.DictReader(f)]

Quick Reference

Tutorial Topics Covered
Graph Construction LZGraph variants, gene annotations, abundance weighting
Sequence Analysis lzpgen, simulate, lz76_decompose
Diversity Metrics k_diversity, hill_numbers, predicted_richness

Next Steps

After completing the tutorials: