Bioconductor – geneplast

DOI: 10.18129/B9.bioc.geneplast  

 

This package is for version 3.13 of Bioconductor;
for the stable, up-to-date release version, see
geneplast.

Evolutionary and plasticity analysis of orthologous groups

Bioconductor version: 3.13

Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.

Author: Rodrigo Dalmolin, Mauro Castro

Maintainer: Mauro Castro <mauro.a.castro at gmail.com>

Citation (from within R,
enter citation("geneplast")):

Installation

To install this package, start R (version
“4.1”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("geneplast")

For older versions of R, please refer to the appropriate
Bioconductor release.

Documentation

To view documentation for the version of this package installed
in your system, start R and enter:

browseVignettes("geneplast")

 

HTML

R Script

Geneplast: evolutionary rooting and plasticity analysis.

HTML

R Script

Supporting Material for Trefflich2019.
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, Genetics, Software, SystemsBiology
Version 1.18.0
In Bioconductor since BioC 3.4 (R-3.3) (5 years)
License GPL (>= 2)
Depends R (>= 3.3), methods
Imports igraph, snow, ape, grDevices, graphics, stats, utils, data.table
LinkingTo
Suggests RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me TreeAndLeaf
Links To Me
Build Report  

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