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Bioconductor - geneplast (development version)

geneplast

This is the development version of geneplast; for the stable release version, see geneplast.

Evolutionary and plasticity analysis of orthologous groups

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews GeneRegulation, Genetics, Software, SystemsBiology Version 1.35.0 In Bioconductor since BioC 3.4 (R-3.3) (8.5 years) License GPL (>= 2) Depends R (>= 4.0), methods Imports igraph, snow, ape, grDevices, graphics, stats, utils, data.table System Requirements URL See More Suggests RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr Linking To Enhances Depends On Me Imports Me geneplast.data Suggests Me TreeAndLeaf, geneplast.data Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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