pepitope facilitates TCR-neoantigen screen analysis in the R language

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ID: 321902
2026
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Abstract
MOTIVATION: Functional screening of patient-derived T cell receptor (TCR)-neoantigen pairs via co-culture experiments is a way to design personalised immunotherapy or to investigate its mechanism of action. Current computational toolkits can either generate and prioritise candidate epitopes from tumour variants or count barcodes in sequencing data. However, they lack modules to support experimental screening, such as sample demultiplexing, construct quality control, and downstream analysis. To bridge these gaps, we present pepitope, an R package that integrates minigene library generation, sequencing-based quality control (QC), and differential abundance analysis of co-culture screens into a single software package within the accessible R/Bioconductor ecosystem. RESULTS: pepitope workflows include the extraction of mutant and reference peptides with customisable flanking regions from tumour variant calls using Bioconductor annotation resources; demultiplexing and barcode counting for construct QC; and negative-binomial-based differential testing built on DESeq2 to identify immunogenic epitopes in TCR co-culture assays. By remaining within R, pepitope lowers the barrier for lab-based biologists familiar with R and Bioconductor to perform end-to-end co-culture screen analyses without needing dedicated computational support. AVAILABILITY: pepitope (R ≥ 4.5.0) is freely available on GitHub under the GPL-3.0 license, with detailed vignettes hosted at https://mschubert.github.io/pepitope/. Installation is facilitated via the remotes package in R. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W7170044385 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Moritz Broft, Wouter Scheper, Michaël Schubert
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag542
URL
https://doi.org/10.1093/bioinformatics/btag542
Keywords Keywords not found

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