MetaEntropy: Functional Shannon Entropy for Virome Mutational Analysis

Estimates Shannon entropy, per gene and per genomic position, associated with non-synonymous mutation frequencies in viral populations, such as wastewater samples. The package uses codon translations for functional insights. Each amino acid can be treated as an individual state, resulting in a 20-state entropy computation, or grouped into one of six physicochemical classes, adding further functional context. 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.

Version:	1.3
Depends:	R (≥ 4.1.0)
Imports:	ggplot2, patchwork, beeswarm, knitr
Suggests:	rmarkdown
Published:	2026-03-09
DOI:	10.32614/CRAN.package.MetaEntropy
Author:	Leandro Roberto Jones [aut, cre], Julieta Marina Manrique [aut]
Maintainer:	Leandro Roberto Jones <lrj000 at gmail.com>
License:	MIT + file LICENSE
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	MetaEntropy results

Documentation:

Reference manual:	MetaEntropy.html , MetaEntropy.pdf
Vignettes:	Overview of MetaEntropy (source, R code)

Downloads:

Package source:	MetaEntropy_1.3.tar.gz
Windows binaries:	r-devel: MetaEntropy_1.3.zip, r-release: MetaEntropy_1.2.zip, r-oldrel: MetaEntropy_1.2.zip
macOS binaries:	r-release (arm64): MetaEntropy_1.3.tgz, r-oldrel (arm64): MetaEntropy_1.3.tgz, r-release (x86_64): MetaEntropy_1.3.tgz, r-oldrel (x86_64): MetaEntropy_1.3.tgz
Old sources:	MetaEntropy archive

Linking:

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