immApex

May 7, 2026 · View on GitHub

API for single-cell immune repertoire deep learning models

Introduction

Single-cell sequencing is now a integral tool in the field of immunology and oncology that allows researchers to couple RNA quantification and other modalities, like immune cell receptor profiling at the level of an individual cell. Towards this end, we developed the scRepertoire R package to assist in the interaction of immune receptor and gene expression sequencing. Further we developed models for embedding single-cell TCR sequences (Trex) and BCR sequences (Ibex) using convolutional neural networks. immApex is the API for preparing the sequence data for the current and future models in the scRepertoire ecosystem. In addition, immApex serves as a general toolbox for prepping and running immune-receptor-based sequences through R to develop machine-learning and deep-learning algorithms.

System requirements

immApex has been tested on R versions >= 4.0. Please consult the DESCRIPTION file for more details on required R packages - it is specifically designed to work with single-cell objects that have had BCR/TCRs added using scRepertoire. immApex has been tested on OS X and Linux platforms.

Installation

To run immApex, open R and install immApex from github:

devtools::install_github("BorchLab/immApex")

or via Bioconductor with the 3.20 release

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("immApex")

Installing immReferent

immApex requires immReferent for IMGT reference sequence access. immReferent will be available via Bioconductor in the next release. Until then, install it from GitHub:

devtools::install_github("BorchLab/immReferent")

IMGT usage

IMGT is used as a reference for gene names and sequence information can be accessed via getIMGT(), which uses immReferent for downloading and locally caching reference sequences. Data from IMGT is under a CC BY-NC-ND 4.0 license. Please be aware that attribution is required for usage and it is the intent of IMGT to not allow derivative or commercial usage.

If you run into any issues or bugs please submit a GitHub issue with details of the issue.

If possible please include a reproducible example.

Any requests for new features or enhancements can also be submitted as GitHub issues.

Pull Requests are welcome for bug fixes, new features, or enhancements.

Citation

If you use immApex in your work, please cite:

Borcherding N, et al. (2026). Pre-transplant TCR Network Topology Predicts Kidney Allograft Rejection Independent of HLA Mismatch. bioRxiv. doi: 10.64898/2026.05.04.722749