geneplast: Evolutionary and plasticity analysis based on orthologous groups distribution
Version 1.2.0

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.

AuthorRodrigo Dalmolin, Mauro Castro
Bioconductor views GeneRegulation Genetics SystemsBiology
Date of publicationNone
MaintainerMauro Castro <mauro.a.castro@gmail.com>
LicenseGPL (>= 2)
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("geneplast")

Getting started

Package overview

Popular 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.
groot.get: Get information from individual slots in an OGR object.
groot.preprocess: Evolutionary rooting inference.
OGR-class: Class '"OGR"': an S4 class for rooting analysis.
See all...

All man pages Function index File listing

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.

Functions

OGP-class Man page
OGR-class Man page
areColors Source code
brmethod Source code
cogAbundance Source code
cogDiversity Source code
droot Source code
epidx Source code
gedAdjDscore Source code
geneplast Man page
geneplast-package Man page
geneplast.checks Source code
getBranches Source code
getLCAs Source code
getprobs Source code
gpdata.gs Man page
gplast Man page
gplast,OGP-method Man page
gplast.get Man page
gplast.get,OGP-method Man page
gplast.preprocess Man page Source code
groot Man page
groot,OGR-method Man page
groot.get Man page
groot.get,OGR-method Man page
groot.plot Man page Source code
groot.preprocess Man page Source code
isParallel Source code
ksmethod Source code
orthoCount Source code
plot.lcas Source code
plot.phylo Source code
rootCount Source code
rotatePhyloTree Source code
runPermutation Source code
spBranches Source code
tipOrder Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllChecks.R
R/AllClasses.R
R/AllContructors.R
R/AllGenerics.R
R/AllMethods.R
R/AllPlots.R
R/AllSupplements.R
build
build/vignette.rds
data
data/datalist
data/gpdata.gs.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/geneplast.R
inst/doc/geneplast.Rnw
inst/doc/geneplast.pdf
inst/unitTests
inst/unitTests/test_gp.R
man
man/OGP-class.Rd
man/OGR-class.Rd
man/geneplast-package.Rd
man/gpdata.Rd
man/gplast.Rd
man/gplast.get.Rd
man/gplast.preprocess.Rd
man/groot.Rd
man/groot.get.Rd
man/groot.plot.Rd
man/groot.preprocess.Rd
tests
tests/runTests.R
vignettes
vignettes/Bioc.bib
vignettes/Fig1.pdf
vignettes/Fig2.pdf
vignettes/geneplast.Rnw
geneplast documentation built on May 20, 2017, 10:05 p.m.

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