geneplast

DOI: 10.18129/B9.bioc.geneplast    

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

Evolutionary and plasticity analysis based on orthologous groups distribution

Bioconductor version: Development (3.8)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("geneplast")

Documentation

HTML R Script Geneplast: evolutionary rooting and plasticity analysis.
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, Genetics, Software, SystemsBiology
Version 1.7.0
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.3), methods
Imports igraph, snow, ape, grDevices, graphics, stats, utils
LinkingTo
Suggests RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package geneplast_1.7.0.tar.gz
Windows Binary geneplast_1.7.0.zip
Mac OS X 10.11 (El Capitan) geneplast_1.7.0.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 http://bioconductor.org/packages/geneplast/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: