Package: MetaEntropy 1.4

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.

Authors:Leandro Roberto Jones [aut, cre], Julieta Marina Manrique [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetaEntropy/json (API)

# Install 'MetaEntropy' in R:
install.packages('MetaEntropy', repos = c('https://jones-lr.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • intraHostVariants - SNVs from multiple organs of individuals with postmortem SARS-CoV-2 detection
  • mn908947.3 - CDS topology and length of Wuhan-Hu-1 reference strain
  • wWater - Data from first and third COVID-19 waves in Trelew <http://tools.wmflabs.org/geohack/geohack.php?language=es&pagename=Trelew&params=-43.253333333333_N_-65.309444444444_E_type:city>

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.48 score 244 downloads 4 exports 34 dependencies

Last updated from:9fdb9ebe35. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK120
source / vignettesOK165
linux-releaseOK127
macos-releaseOK179
macos-oldrelOK160
windows-develOK88
windows-releaseOK80
windows-oldrelOK74
wasm-releaseOK96

Exports:assessHotSpotgetEntropySignatureheatmap_entropyProfilesshowMutations

Dependencies:beeswarmclicpp11dplyrevaluatefarvergenericsggbeeswarmggplot2gluegtablehighrisobandknitrlabelinglifecyclemagrittrpatchworkpillarpkgconfigR6RColorBrewerrlangS7scalestibbletidyselectutf8vctrsviporviridisLitewithrxfunyaml

intraHostVariants: SNVs from Multiple Anatomical Sites
Introduction | Data Structure and Characteristics | Package Integration | Create a custom genome | Entropy computation | Profiles comparison | References
Rendered fromintraHostVariants.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2026-09-03

Overview of MetaEntropy
Motivation | Input data | Worked example: SARS-CoV-2 immune escape | Loading packages | Conceptual framework and data | Entropy signatures | Omicron sublineages in more detail | Integrating Biological Signal via Entropy | References
Rendered fromoverview.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2026-03-03