geneplast
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see geneplast.
Evolutionary and plasticity analysis of orthologous groups
Bioconductor version: 3.13
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("geneplast")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneRegulation, Genetics, Software, SystemsBiology |
| Version | 1.18.0 |
| 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 |
See More
| Suggests | RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | TreeAndLeaf |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | geneplast_1.18.0.tar.gz |
| Windows Binary | geneplast_1.18.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | geneplast_1.18.0.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 3.13 | Source Archive |