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geneplast

Evolutionary and plasticity analysis of orthologous groups


Bioconductor version: Release (3.19)

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 "4.4") and enter:


if (!require("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")
Geneplast: evolutionary analysis of orthologous groups. HTML R Script
Supporting Material for Trefflich2019. HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneRegulation, Genetics, Software, SystemsBiology
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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.

Source Package geneplast_1.30.0.tar.gz
Windows Binary geneplast_1.30.0.zip (64-bit only)
macOS Binary (x86_64) geneplast_1.30.0.tgz
macOS Binary (arm64) geneplast_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/geneplast
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/geneplast
Bioc Package Browser https://code.bioconductor.org/browse/geneplast/
Package Short Url https://bioconductor.org/packages/geneplast/
Package Downloads Report Download Stats