geneplast

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see geneplast.

Evolutionary and plasticity analysis of orthologous groups


Bioconductor version: 3.10

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 "3.6") 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 rooting and plasticity analysis. HTML R Script
Supporting Material for Trefflich2019. HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneRegulation, Genetics, Software, SystemsBiology
Version 1.12.2
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL (>= 2)
Depends R (>= 3.3), methods
Imports igraph, snow, ape, grDevices, graphics, stats, utils, data.table
System Requirements
URL
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Suggests RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr
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Package Archives

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

Source Package geneplast_1.12.2.tar.gz
Windows Binary geneplast_1.12.2.zip
Mac OS X 10.11 (El Capitan) geneplast_1.12.2.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
Old Source Packages for BioC 3.10 Source Archive