GeneGA: Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
Version 1.26.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorZhenpeng Li and Haixiu Huang
Bioconductor views GeneExpression
Date of publicationNone
MaintainerZhenpeng Li <zpli21@gmail.com>
LicenseGPL version 2
Version1.26.0
URL http://www.tbi.univie.ac.at/~ivo/RNA/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneGA")

Man pages

GeneCodon: Optimizing the codon usage of gene by replacing less usage...
GeneFoldGA: the function optimizes gene merely considering mRNA secondary...
GeneFoldGA-class: Class "GeneFoldGA"
GeneGA: the function optimizes gene expression based on both mRNA...
GeneGA-class: Class "GeneGA"
GeneGA-package: Designing gene based on mRNA secondary structure and codon...
plotGeneGA-methods: plotGeneGA methods of GeneGA and GeneFoldGA objects
wSet: Codon Adaptation Index (CAI) w tables

Functions

GeneCodon Man page Source code
GeneFoldGA Man page Source code
GeneFoldGA-class Man page
GeneGA Man page Source code
GeneGA-class Man page
GeneGA-package Man page
GeneGA_internal Source code
evaluationFoldFunction Source code
evaluationFunction Source code
evaluationFunction_internal Source code
fold Source code
plotGeneGA Man page
plotGeneGA,GeneFoldGA-method Man page
plotGeneGA,GeneGA-method Man page
plotGeneGA-methods Man page
plotGeneGA.GeneFoldGA Man page
plotGeneGA.GeneGA Man page
show,GeneFoldGA-method Man page
show,GeneGA-method Man page
wSet Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/GeneCodon.R
R/GeneFoldGA.R
R/GeneGA-internal.R
R/GeneGA.R
R/GeneGA_internal.R
R/evaluationFunction.R
build
build/vignette.rds
data
data/wSet.rda
inst
inst/doc
inst/doc/GeneGA.R
inst/doc/GeneGA.Rnw
inst/doc/GeneGA.pdf
inst/sequence
inst/sequence/EGFP.fasta
man
man/GeneCodon.Rd
man/GeneFoldGA-class.Rd
man/GeneFoldGA.Rd
man/GeneGA-class.Rd
man/GeneGA-package.Rd
man/GeneGA.Rd
man/plotGeneGA-methods.Rd
man/wSet.Rd
vignettes
vignettes/GeneGA.Rnw
vignettes/GeneGA.bib
GeneGA documentation built on May 20, 2017, 9:37 p.m.