Package: geneplast 1.33.0

Mauro Castro

geneplast: Evolutionary and plasticity analysis of orthologous groups

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.

Authors:Rodrigo Dalmolin, Mauro Castro

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geneplast.pdf |geneplast.html✨
geneplast/json (API)
NEWS

# Install 'geneplast' in R:
install.packages('geneplast', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • gpdata.gs - A pre-processed dataset for the geneplast package.
  • ppi.gs - A pre-processed igraph object for the geneplast package.

On BioConductor:geneplast-1.31.0(bioc 3.20)geneplast-1.30.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneticsgeneregulationsystemsbiology

4.11 score 16 scripts 234 downloads 2 mentions 9 exports 17 dependencies

Last updated 23 days agofrom:e60530e504. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:gplastgplast.getgplast.preprocessgrootgroot.getgroot.plotgroot.preprocessogr2igraphogr2tni

Dependencies:apeclicpp11data.tabledigestglueigraphlatticelifecyclemagrittrMatrixnlmepkgconfigRcpprlangsnowvctrs

Geneplast: large-scale evolutionary analysis of orthologous groups.

Rodrigo JS Dalmolin, Sheyla Trefflich, Diego AA Morais, Mauro AA Castro.

Rendered fromgeneplast.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-08-15
Started: 2018-01-23

Supporting Material for Trefflich2019

Sheyla Trefflich, Rodrigo J. S. Dalmolin, José M. Ortega, Mauro A. A. Castro.

Rendered fromgeneplast_Trefflich2019.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-11-05
Started: 2019-05-24