Package: ggrasp 1.2

ggrasp: Gaussian-Based Genome Representative Selector with Prioritization

Given a group of genomes and their relationship with each other, the package clusters the genomes and selects the most representative members of each cluster. Additional data can be provided to the prioritize certain genomes. The results can be printed out as a list or a new phylogeny with graphs of the trees and distance distributions also available. For detailed introduction see: Thomas H Clarke, Lauren M Brinkac, Granger Sutton, and Derrick E Fouts (2018), GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models, Bioinformatics, bty300, <doi:10.1093/bioinformatics/bty300>.

Authors:Thomas Clarke [aut, cre]

ggrasp_1.2.tar.gz
ggrasp_1.2.zip(r-4.5)ggrasp_1.2.zip(r-4.4)ggrasp_1.2.zip(r-4.3)
ggrasp_1.2.tgz(r-4.4-any)ggrasp_1.2.tgz(r-4.3-any)
ggrasp_1.2.tar.gz(r-4.5-noble)ggrasp_1.2.tar.gz(r-4.4-noble)
ggrasp_1.2.tgz(r-4.4-emscripten)ggrasp_1.2.tgz(r-4.3-emscripten)
ggrasp.pdf |ggrasp.html
ggrasp/json (API)
NEWS

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

Peer review:

On CRAN:

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

2.06 score 23 scripts 171 downloads 5 exports 100 dependencies

Last updated 3 years agofrom:fcca5a22cb. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 14 2024
R-4.5-winOKOct 14 2024
R-4.5-linuxOKOct 14 2024
R-4.4-winOKOct 14 2024
R-4.4-macOKOct 14 2024
R-4.3-winOKOct 14 2024
R-4.3-macOKOct 14 2024

Exports:ggrasp.addRanksggrasp.clusterggrasp.loadggrasp.reclusterggrasp.write

Dependencies:abindapeaskpassbackportsbase64encbgmmbootbroombslibcachemcarcarDataclicolorspacecombinatcowplotcpp11crosstalkcurldata.tableDerivdigestdoBydplyrevaluatefansifarverfastmapfontawesomeFormulafsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamixtoolsmodelrmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotlypromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownsassscalessegmentedSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
An S4 class representing the GGRaSP data and outputggrasp-class
ggrasp.addRanksggrasp.addRanks
ggrasp.clusterggrasp.cluster
ggrasp.loadggrasp.load
ggrasp.reclusterggrasp.recluster
ggrasp.writeggrasp.write
plot.ggraspplot.ggrasp
print.ggraspprint.ggrasp
summary.ggraspsummary.ggrasp