immundata 0.1.1.dev0

A data layer for single-cell, spatial and bulk immunomics, providing a unified structure for immune receptor repertoire data.

immundata-py

An efficient data framework for single-cell and bulk immune repertoire datasets of practically any scale.

Think AnnData, SingleCellExperiment or Seurat object, but for AIRR with the full support for out-of-memory datasets and easier access to additional receptor data such as gene expression from single-cell transcriptomics files, spatial data coordinates, or antigen specificity data, provided by user. The goal of immundata is to standardize I/O and basic data manipulation, following the AIRR Community Data Standard for immune repertoire representation. It's primary users are bioinformatics developers and data engineers who don't want to write from scratch an abstraction layer over the data. Biologists and medical scientists could benefit as well, considering they learn the code syntaxis. However, the overall philosophy is to make sure that immune repertoire data analysis tools such as immunarch cover more than 80% of use cases without explicitly using immundata by the end user.

Installation

uv install

Usage

See notebooks/immundata-experiments.ipynb.