Evolutionary and plasticity analysis of orthologous groups

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Documentation for package ‘geneplast’ version 1.32.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

geneplast-package	Geneplast: an R package for evolutionary rooting and plasticity inference based on orthologous groups distribution.
geneplast	Geneplast: an R package for evolutionary rooting and plasticity inference based on orthologous groups distribution.
gpdata.gs	A pre-processed dataset for the geneplast package.
gplast	Evolutionary plasticity inference.
gplast-method	Class '"OGP"': an S4 class for genetic plasticity analysis.
gplast.get	Get information from individual slots in an OGP object.
gplast.get-method	Class '"OGP"': an S4 class for genetic plasticity analysis.
gplast.preprocess	Evolutionary plasticity inference.
groot	Evolutionary rooting inference.
groot-method	Class '"OGR"': an S4 class for rooting analysis.
groot.get	Get information from individual slots in an OGR object.
groot.get-method	Class '"OGR"': an S4 class for rooting analysis.
groot.integration-method	Class '"OGR"': an S4 class for rooting analysis.
groot.plot	Plot the inferred evolutionary root of a given OG or the map of LCAs of a given species.
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.
ogr2igraph	Integrates evolutionary rooting information and graphs.
ogr2tni	Integrates evolutionary rooting information and regulatory networks.
ppi.gs	A pre-processed igraph object for the geneplast package.