Abstract
Summary B cells are critical for adaptive immunity and are governed by the recognition of an antigen by the B cell receptor (BCR), a process that drives a coordinated series of signaling events and modulation of various transcriptional programs. Single-cell RNA sequencing with paired BCR profiling could offer insights into numerous physiological and pathological processes. However, unlike the plethora of single-cell RNA analysis pipelines, computational tools that utilize single-cell BCR sequences for further analyses are not yet well developed. Here we report Ibex, which vectorizes the amino acid sequence of the complementarity-determining region 3 (cdr3) of the immunoglobulin heavy and light chains, allowing for unbiased dimensional reduction of B cells using their BCR repertoire. Ibex is implemented as an R package with integration into both the Seurat and Single-Cell Experiment framework, enabling the incorporation of this new analytic tool into many single-cell sequencing analytic workflows and multimodal experiments.
Availability and Implementation Ibex is available as an R package at https://github.com/ncborcherding/Ibex. Reproducible code and data for the figure appearing in the manuscript are available at https://github.com/ncborcherding/Ibex.manuscript. A companion TCR-based approach is available at https://github.com/ncborcherding/Trex.
Competing Interest Statement
NB is a consultant for Santa Ana Bio, Inc and Omniscope, Inc. The results outlined in this publication are independent of these interests.
Footnotes
Per reviewer comments, supplemental materials have been included to allow users to 1) evaluate use of models, 2) understand model development, and 3) compare to alternative pipelines.