geneplast
Evolutionary and plasticity analysis of orthologous groups
Bioconductor version: 3.23 · Package version: 1.38.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("geneplast")Details
| Maintainer | Mauro Castro <mauro.a.castro@gmail.com> |
| Author | Rodrigo Dalmolin, Mauro Castro |
| License | GPL (>= 2) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneRegulation, Genetics, Software, SystemsBiology |
| Package Short Url | https://bioconductor.org/packages/geneplast/ |
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.
Documentation
- Geneplast: large-scale evolutionary analysis of orthologous groups.
- Supporting Material for Trefflich2019
Download
Follow the 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 |
| macOS binary (arm64) | geneplast_1.38.0.tgz |
| macOS binary (x86_64) | geneplast_1.38.0.tgz |
Dependencies
Depends: R (>= 4.0), methods
Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table
Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr