geneplast

This is the released version of geneplast; for the devel version, see geneplast.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Evolutionary and plasticity analysis of orthologous groups

Bioconductor version: Release (3.23)

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")):

Rodrigo Dalmolin, Mauro Castro. geneplast: Evolutionary and plasticity analysis of orthologous groups. doi:10.18129/B9.bioc.geneplast, R package version 1.38.0, https://bioconductor.org/packages/geneplast.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneRegulation, Genetics, Software, SystemsBiology
Version	1.38.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	GPL (>= 2)
Depends	R (>= 4.0), methods
Imports	igraph, snow, ape, grDevices, graphics, stats, utils, data.table
System Requirements
URL

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	geneplast.data
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	geneplast_1.38.0.tar.gz
Windows Binary (x86_64)	geneplast_1.38.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	geneplast_1.38.0.tgz
macOS Binary (sonoma-arm64)	geneplast_1.38.0.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