geneplast: Evolutionary and plasticity analysis based on orthologous groups distribution

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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
Date of publication
None
Maintainer
Mauro Castro <mauro.a.castro@gmail.com>
License
GPL (>= 2)
Version
1.0.0

View on Bioconductor

Man pages

geneplast-package
Geneplast: an R package for evolutionary rooting and...
gpdata
A pre-processed dataset for the geneplast package.
gplast
Evolutionary plasticity inference.
gplast.get
Get information from individual slots in an OGP object.
gplast.preprocess
Evolutionary plasticity inference.
groot
Evolutionary rooting inference.
groot.get
Get information from individual slots in an OGR object.
groot.plot
Plot the inferred evolutionary root of a given OG or the map...
groot.preprocess
Evolutionary rooting inference.
OGP-class
Class '"OGP"': an S4 class for genetic plasticity analysis.
OGR-class
Class '"OGR"': an S4 class for rooting analysis.

Files in this package

geneplast/DESCRIPTION
geneplast/NAMESPACE
geneplast/R
geneplast/R/AllChecks.R
geneplast/R/AllClasses.R
geneplast/R/AllContructors.R
geneplast/R/AllGenerics.R
geneplast/R/AllMethods.R
geneplast/R/AllPlots.R
geneplast/R/AllSupplements.R
geneplast/build
geneplast/build/vignette.rds
geneplast/data
geneplast/data/datalist
geneplast/data/gpdata.gs.RData
geneplast/inst
geneplast/inst/CITATION
geneplast/inst/NEWS.Rd
geneplast/inst/doc
geneplast/inst/doc/geneplast.R
geneplast/inst/doc/geneplast.Rnw
geneplast/inst/doc/geneplast.pdf
geneplast/inst/unitTests
geneplast/inst/unitTests/test_gp.R
geneplast/man
geneplast/man/OGP-class.Rd
geneplast/man/OGR-class.Rd
geneplast/man/geneplast-package.Rd
geneplast/man/gpdata.Rd
geneplast/man/gplast.Rd
geneplast/man/gplast.get.Rd
geneplast/man/gplast.preprocess.Rd
geneplast/man/groot.Rd
geneplast/man/groot.get.Rd
geneplast/man/groot.plot.Rd
geneplast/man/groot.preprocess.Rd
geneplast/tests
geneplast/tests/runTests.R
geneplast/vignettes
geneplast/vignettes/Bioc.bib
geneplast/vignettes/Fig1.pdf
geneplast/vignettes/Fig2.pdf
geneplast/vignettes/geneplast.Rnw