Package: MetaEntropy
Title: Functional Shannon Entropy for Virome Mutational Analysis
Version: 1.2
Date: 2026-02-09
Authors@R: c( person("Leandro Roberto", "Jones", email = "lrj000@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5877-4194")),
    person("Julieta Marina", "Manrique", role = c("aut"), comment = c(ORCID = "0000-0001-8712-6666")))
Description: Estimates Shannon entropy, per gene and per genomic position,
    associated with non-synonymous mutation frequencies in viral populations,
    such as wastewater samples or quasispecies. By categorizing amino acids
    based on their physicochemical properties, the package determines whether a
    mutation is functionally disruptive or neutral. Provides normalized values
    (0-1 scale) to facilitate the direct comparison of different genomic
    positions or total functional entropy across multiple metagenomes. Designed
    to analyze mutational data using tabular 'Single Nucleotide Variant' (SNV)
    frequency tables generated by variant callers (e.g., 'iVar' or 'LoFreq'),
    operating independently of consensus sequence estimation and multiple
    sequence alignment.
Encoding: UTF-8
Depends: R (>= 4.1.0)
LazyData: true
Suggests: rmarkdown
Imports: ggplot2, patchwork, beeswarm, knitr
VignetteBuilder: knitr
RoxygenNote: 7.3.3
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2026-02-24 18:36:01 UTC; leandro
Author: Leandro Roberto Jones [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5877-4194>),
  Julieta Marina Manrique [aut] (ORCID:
    <https://orcid.org/0000-0001-8712-6666>)
Maintainer: Leandro Roberto Jones <lrj000@gmail.com>
Repository: CRAN
Date/Publication: 2026-03-03 10:00:38 UTC
