replicateFest: an R package and shiny app for analysis of T cell receptor repertoire data from the functional expansion.
- 1Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States.
- 2Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States.
Abstract
Motivation
The Functional Expansion of Specific T cell (FEST)-based assays combine short-term peptide stimulation with TCR sequencing to identify clonotypes that expand in response to specific antigens. These approaches have proven invaluable for detecting antigen-specific T cell responses, guiding vaccine development, and assessing checkpoint blockade efficacy. However, variability introduced by biological and technical replicates poses challenges for reproducibility and interpretation, and existing computational tools do not address replicate-level analysis in these assays.Results
We developed replicateFest, a computational framework implemented as an R package and Shiny web application, to analyze FEST-based TCR-seq data with and without replicates. replicateFest applies Fisher's exact test for non-replicate datasets and negative binomial modeling for replicate experiments, returning adjusted p-values and odds ratios to identify clonotypes significantly expanded in antigen-stimulated conditions. The framework distinguishes FEST-expanded clonotypes (relative to a no-antigen control) and FEST-positive clonotypes (expanded compared to all other conditions). Validation using in silico datasets confirmed accurate detection of antigen-specific clonotypes. Application to published HIV-1 epitope stimulation data reproduced original findings and demonstrated replicateFest's utility for reproducibility assessment and quality control.
Related
- Gene repertoire expansion and cis-regulatory diversification shaped 26S proteasome evolution within a proteostasis-centered network
- A computable probability landscape for T cell receptor repertoire sampling and comparison
- ClonoDynamics enables replicate-resolved inference of longitudinal T cell receptor repertoire dynamics
- EMMA: an R/Bioconductor package to automate tracking of metadata in functional enrichment analyses
- Sensory receptor expansion and neural accommodation in butterfly color vision
BibTeX
@article{danilova2026replicatefest,
title = {{replicateFest: an R package and shiny app for analysis of T cell receptor repertoire data from the functional expansion.}},
author = {Ludmila Danilova and Alexander V Favorov and Kellie N Smith and Leslie Cope},
journal = {Frontiers in immunology},
year = {2026},
month = oct,
doi = {10.3389/fimmu.2026.1937788},
url = {https://europepmc.org/article/MED/42890172},
note = {CC BY},
}
RIS
TY - JOUR
TI - replicateFest: an R package and shiny app for analysis of T cell receptor repertoire data from the functional expansion.
AU - Ludmila Danilova
AU - Alexander V Favorov
AU - Kellie N Smith
AU - Leslie Cope
PY - 2026
DA - 2026/10/02
JO - Frontiers in immunology
DO - 10.3389/fimmu.2026.1937788
UR - https://europepmc.org/article/MED/42890172
AB - Motivation The Functional Expansion of Specific T cell (FEST)-based assays combine short-term peptide stimulation with TCR sequencing to identify clonotypes that expand in response to specific antigens. These approaches have proven invaluable for detecting antigen-specific T cell responses, guiding vaccine development, and assessing checkpoint blockade efficacy. However, variability introduced by biological and technical replicates poses challenges for reproducibility and interpretation, and existing computational tools do not address replicate-level analysis in these assays.Results We developed replicateFest, a computational framework implemented as an R package and Shiny web application, to analyze FEST-based TCR-seq data with and without replicates. replicateFest applies Fisher's exact test for non-replicate datasets and negative binomial modeling for replicate experiments, returning adjusted p-values and odds ratios to identify clonotypes significantly expanded in antigen-stimulated conditions. The framework distinguishes FEST-expanded clonotypes (relative to a no-antigen control) and FEST-positive clonotypes (expanded compared to all other conditions). Validation using in silico datasets confirmed accurate detection of antigen-specific clonotypes. Application to published HIV-1 epitope stimulation data reproduced original findings and demonstrated replicateFest's utility for reproducibility assessment and quality control.
SN - 1664-3224
ER -