A Computational Pipeline for Entropy-Informed Detection of Emerging Viral Variants R package ViralEntropR version 0.6.2 Implements an entropy-informed pipeline for detecting emerging variants in viral amino acid sequence data, extending prior clustering-based approaches including hemagglutinin clustering methods (Li et al., 2015) <doi:10.1142/9789814667944_0018>. Provides a fully vectorized FASTA preprocessing toolkit covering header parsing, two-pass date and country extraction, ambiguous-residue filtering, and integer encoding under a 25-symbol amino acid alphabet. Computes per-site Shannon entropy across user-defined cumulative, sliding, or disjoint temporal partitions and clusters per-site entropy values using Gaussian mixture models via 'mclust' (Scrucca et al., 2016) <doi:10.32614/RJ-2016-021>. Quantifies temporal distributional shifts between partitions using the Hellinger distance (van der Vaart, 1998) <doi:10.1017/CBO9780511802256>, and detects temporal change points non-parametrically using energy statistics (Matteson and James, 2014) <doi:10.1080/01621459.2013.849605> via 'ecp' or wild binary segmentation (Fryzlewicz, 2014) <doi:10.1214/14-AOS1245> via 'HDcpDetect'. Per-site amino-acid frequency tables and entropy trajectory plots characterize sequence composition and evolutionary dynamics across time. A configurable multi-variant simulation engine generates synthetic sequence time series with known ground truth for benchmarking detection pipelines. A curated dataset of SARS-CoV-2 Variants of Concern and Variants of Interest with associated lineage and surveillance metadata is included, along with a bundled National Center for Biotechnology Information (NCBI) Spike protein sample and vignettes demonstrating the full workflow. Software Depends: R (>= 3.5.0) Imports: ggplot2 (>= 3.4.0), grDevices, HDcpDetect, ecp, kableExtra, lubridate, magrittr, mclust, rlang, stats, stringr, utils, zoo Suggests: Biostrings, DT, dplyr, here, knitr, readxl, rmarkdown, R.rsp, testthat (>= 3.0.0) Vadim Tyuryaev <vadim.tyuryaev@gmail.com> Comprehensive R Archive Network (CRAN) Vadim Tyuryaev [aut, cre] (ORCID: <https://orcid.org/0009-0008-1361-6265>), Jane Heffernan [aut], Hanna Jankowski [aut] MIT + file LICENSE (https://CRAN.R-project.org/package=ViralEntropR/LICENSE) 2026-05-30 application/tgz https://CRAN.R-project.org/package=ViralEntropR doi:10.32614/CRAN.package.ViralEntropR en-GB