RT Journal Article
SR Electronic
T1 Ibex: Variational autoencoder for single-cell BCR sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.11.09.515787
DO 10.1101/2022.11.09.515787
A1 Nicholas Borcherding
A1 Bo Sun
A1 David DeNardo
A1 Jonathan R. Brestoff
YR 2022
UL http://biorxiv.org/content/early/2022/11/10/2022.11.09.515787.abstract
AB 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.Competing Interest StatementNB is a consultant for Santa Ana Bio, Inc.