geneplast

DOI: 10.18129/B9.bioc.geneplast    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see geneplast.

Evolutionary and plasticity analysis of orthologous groups

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

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	1.22.0
In Bioconductor since	BioC 3.4 (R-3.3) (6 years)
License	GPL (>= 2)
Depends	R (>= 4.0), 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	geneplast.data, TreeAndLeaf
Links To Me
Build Report

Package Archives

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

Source Package	geneplast_1.22.0.tar.gz
Windows Binary	geneplast_1.22.0.zip
macOS Binary (x86_64)	geneplast_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/geneplast
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/geneplast
Package Short Url	https://bioconductor.org/packages/geneplast/
Package Downloads Report	Download Stats