GeneGA
This is the development version of GeneGA; for the stable release version, see GeneGA.
Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
Bioconductor version: Development (3.24)
R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.
Author: Zhenpeng Li and Haixiu Huang
Maintainer: Zhenpeng Li <zpli21 at gmail.com>
citation("GeneGA")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GeneGA")
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("GeneGA")| GeneGA | R Script | |
| Reference Manual |
Details
| biocViews | GeneExpression, Software |
| Version | 1.63.1 |
| In Bioconductor since | BioC 2.7 (R-2.12) (16 years) |
| License | GPL version 2 |
| Depends | seqinr, hash, methods |
| Imports | |
| System Requirements | |
| URL | http://www.tbi.univie.ac.at/~ivo/RNA/ |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GeneGA_1.63.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | GeneGA_1.63.1.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GeneGA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GeneGA |
| Bioc Package Browser | https://code.bioconductor.org/browse/GeneGA/ |
| Package Short Url | https://bioconductor.org/packages/GeneGA/ |
| Package Downloads Report | Download Stats |