Quick Start
===========

Bulk TCR-Seq Data
-----------------

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

.. code-block:: python

   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:

.. code-block:: python

   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:

.. code-block:: bash

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

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