Ibex: Variational autoencoder for single-cell BCR sequencing.

Borcherding, N.; Sun, B.; DeNardo, D.; Brestoff, J.

doi:10.1101/2022.11.09.515787

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bioRxiv · 10.1101/2022.11.09.515787

Ibex: Variational autoencoder for single-cell BCR sequencing.

Borcherding, N.·Sun, B.·DeNardo, D.·Brestoff, J.

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Abstract

SummaryB 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 ImplementationIbex 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.

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Borcherding, N., Sun, B., DeNardo, D., Brestoff, J.. 2022-11-10. Ibex: Variational autoencoder for single-cell BCR sequencing.. https://doi.org/10.1101/2022.11.09.515787

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