Background

A Python package for B cell repertoire analysis and lineage tracking in spatial omics.

Documentation • Github

Background#

In contrast to previously reported bulk or single-cell immune receptor sequencing technologies, the simultaneous acquisition of spatially resolved high-dimensional gene expression profiles and complex immune receptor sequences from the same tissue section presents unique challenges for bioinformatic analysis.

To systematically investigate the spatial organization and clonal dynamics of B cells in the tumor microenvironment, we developed BAITS (B cell repertoire Analysis and lIneage Tracking in Spatial omics), a comprehensive and adaptable computational framework for analyzing spatially resolved BCR sequencing data.

Introduction#

BAITS comprises three core modules:

  • Spatial Transcriptomics (ST) module: identify B lymphocyte aggregates based solely on spatial transcriptomic data

  • Immune Repertoire (IR) module: quantify clonal expansion, clonal degree centrality, and other repertoire features using spatial BCR sequencing data

  • SR module: reveal patterns of clonal migration, expansion, and niche restriction by integrating spatial transcriptomic and BCR data

Installation#

1. Create a conda environment and then install Python >= 3.10,<3.13

conda create --name BAITS python=3.10

2. Pip install BAITS

conda activate BAITS
pip install BAITS

This example is based on a Linux CentOS 7 system

Contribution#

If you found a bug or you want to propose a new feature, please use the issue tracker.

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