Quick Start

Bulk TCR-Seq Data

Here’s a simple example of importing and analyzing bulk TCR-seq data:

import lymphoseq as ls

# Import AIRR-seq data
data = ls.read_immunoseq("path/to/data/")

# Calculate repertoire diversity metrics
diversity = ls.clonality(data)

# Visualize clonal expansion
fig = ls.plot_clonality(data)
fig.show()

10X Single-Cell Data

For 10X Genomics single-cell VDJ data:

import lymphoseq as ls

# Read 10X data
data_10x = ls.read_10x("path/to/10x_data/")

# Merge alpha and beta chains for bulk-style analysis
merged = ls.merge_chains(data_10x)

# Now use any bulk analysis function
clonality = ls.clonality(merged)
diversity = ls.diversity_metrics(merged)

# Search for known antigen specificities
annotated = ls.search_db(merged, databases="all", chain="trb")

# Visualize
fig = ls.plot_top_seqs(merged, top=50)
fig.show()

Command Line Usage

LymphoSeq also provides a command-line interface:

# Import and analyze data
lymphoseq import --input data/ --output results/

# Calculate diversity metrics
lymphoseq analyze clonality --input results/data.parquet --output results/