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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 AAPLZGraph, NDPLZGraph, and NaiveLZGraph from your data.

2. Sequence Analysis

Beginner · 20 minutes

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

3. Diversity Metrics

Intermediate · 15 minutes

Measure repertoire diversity using K1000, LZCentrality, and entropy metrics.

4. Visualization

Intermediate · 20 minutes

Create publication-ready plots for sequence and repertoire analysis.

Prerequisites

Before starting, ensure you have:

Sample Data

All tutorials use example data included with LZGraphs:

import pandas as pd

# Load example TCR repertoire
data = pd.read_csv("Examples/ExampleData1.csv")
print(data.head())

Quick Reference

Tutorial Topics Covered
Graph Construction AAPLZGraph, NDPLZGraph, NaiveLZGraph, gene annotation
Sequence Analysis walk_probability, random_walk, encode_sequence, clean_node
Diversity Metrics K1000_Diversity, LZCentrality, node_entropy, edge_entropy
Visualization Ancestors/descendants plots, path variability, genomic heatmaps

Next Steps

After completing the tutorials: