Package: geneplast 1.38.0

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

geneplast_1.38.0.tar.gz
geneplast_1.38.0.zip(r-4.7-any)geneplast_1.38.0.zip(r-4.6-any)geneplast_1.38.0.zip(r-4.5-any)
geneplast_1.38.0.tgz(r-4.6-any)geneplast_1.38.0.tgz(r-4.5-any)
geneplast_1.38.0.tar.gz(r-4.7-any)geneplast_1.38.0.tar.gz(r-4.6-any)
geneplast_1.38.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geneplast/json (API)

# Install 'geneplast' in R:
install.packages('geneplast', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • ppi.gs - A pre-processed igraph object for the geneplast package.

On BioConductor:geneplast-1.39.0(bioc 3.24)geneplast-1.38.0(bioc 3.23)

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

geneticsgeneregulationsystemsbiology

4.16 score 18 scripts 2 mentions 9 exports 17 dependencies

Last updated from:fcc4ac567d (on RELEASE_3_23). Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksFAILURE246
linux-devel-x86_64NOTE336
source / vignettesOK332
linux-release-x86_64NOTE306
macos-release-arm64NOTE131
macos-oldrel-arm64NOTE123
windows-devel-x86_64NOTE439
windows-release-x86_64NOTE464
windows-oldrel-x86_64NOTE366
wasm-releaseOK225

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

Dependencies:apeclicpp11data.tabledigestglueigraphlatticelifecyclemagrittrMatrixnlmepkgconfigRcpprlangsnowvctrs

Geneplast: large-scale evolutionary analysis of orthologous groups.
Overview | Quick start | Evolutionary diversity and abundance | Evolutionary rooting | Case studies | High-throughput rooting inference | Map rooting annotation to PPI networks | Map rooting annotation to regulatory networks | Runtime performance of the rooting pipeline | Orthology data packages | Session information | References
Rendered fromgeneplast.Rmdusingknitr::rmarkdown

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

Supporting Material for Trefflich2019
Context | Package installation and data sets | Inferring evolutionary roots | Evolutionary analysis of regulons generated from breast cancer samples | Mapping root-to-gene annotation | Comparing regulators and targets | Comparing transcription factors and transcription co-factors | Exploring abundance, diversity and plasticity | Evolutionary analysis of regulons generated from normal breast tissue samples | Session information | References
Rendered fromgeneplast_Trefflich2019.Rmdusingknitr::rmarkdown

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