geneplast

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see geneplast.

Evolutionary and plasticity analysis of orthologous groups

Bioconductor version: 3.9

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneRegulation, Genetics, Software, SystemsBiology

Version 1.10.3

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

System Requirements

URL

Suggests RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr

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Package Archives

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

Source Package geneplast_1.10.3.tar.gz

Windows Binary geneplast_1.10.3.zip

Mac OS X 10.11 (El Capitan) geneplast_1.10.3.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 3.9 Source Archive