# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "ViralEntropR" in publications use:' type: software license: MIT title: 'ViralEntropR: A Computational Pipeline for Entropy-Informed Detection of Emerging Viral Variants' version: 0.6.2 identifiers: - type: url value: https://vadimtyuryaev.github.io/ViralEntropR/ abstract: 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) . 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) . Quantifies temporal distributional shifts between partitions using the Hellinger distance (van der Vaart, 1998) , and detects temporal change points non-parametrically using energy statistics (Matteson and James, 2014) via 'ecp' or wild binary segmentation (Fryzlewicz, 2014) 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. authors: - family-names: Tyuryaev given-names: Vadim email: vadim.tyuryaev@gmail.com orcid: https://orcid.org/0009-0008-1361-6265 - family-names: Heffernan given-names: Jane email: jmheffer@yorku.ca - family-names: Jankowski given-names: Hanna email: hkj@yorku.ca repository: https://cran.r-universe.dev repository-code: https://github.com/vadimtyuryaev/ViralEntropR commit: a9b293057a1d5b20f074216fc899da6ebdd0389b url: https://doi.org/10.5281/zenodo.19040165 date-released: '2026-05-07' contact: - family-names: Tyuryaev given-names: Vadim email: vadim.tyuryaev@gmail.com orcid: https://orcid.org/0009-0008-1361-6265