Package: orthGS 0.1.8

orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants

Tools to analyze and infer orthology and paralogy relationships between glutamine synthetase proteins in seed plants.

Authors:Elena Aledo [aut, cre, cph], Juan-Carlos Aledo [aut]

orthGS_0.1.8.tar.gz
orthGS_0.1.8.zip(r-4.7-any)orthGS_0.1.8.zip(r-4.6-any)orthGS_0.1.8.zip(r-4.5-any)
orthGS_0.1.8.tgz(r-4.6-any)orthGS_0.1.8.tgz(r-4.5-any)
orthGS_0.1.8.tar.gz(r-4.7-any)orthGS_0.1.8.tar.gz(r-4.6-any)
orthGS_0.1.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
orthGS/json (API)

# Install 'orthGS' in R:
install.packages('orthGS', repos = c('https://ealedo.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • A_selected - Adjacency Matrix for Orthology Graph
  • agf - Angiosperms Gymnosperms Ferns
  • AngGym - Angiosperms Gymnosperms
  • sdf - Seed Plants and Ferns GS
  • selected_tr - Ultrametric Rooted Seed Plants Tree

On CRAN:

Conda:

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

4.05 score 56 scripts 388 downloads 12 exports 53 dependencies

Last updated from:df5ff31aa5. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK151
source / vignettesOK221
linux-release-x86_64OK169
macos-release-arm64OK275
macos-oldrel-arm64OK150
windows-develOK104
windows-releaseOK129
windows-oldrelOK106
wasm-releaseOK133

Exports:coltipsgapless_msagetseqGSmadRootmapTreesmltreemsaorthGorthologyorthPspeciesGSsubsetGS

Dependencies:ade4apebio3dbitbit64castorcliclusterGenerationcodacodetoolscombinatcpp11DEoptimdigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorsjsonlitelatticelifecyclemagrittrmapsMASSMatrixmnormtnaturalsortnlmenumDerivoptimParallelphangornphytoolspixmappkgconfigPlotToolsquadprogrbibutilsRcppRcppArmadilloRcppEigenRdpackrlangRSpectrascatterplot3dsegmentedseqinrspTreeToolsvctrs

Orthology Beyond GS
What happen if I am interested in a gene family other than GS? | A toy example
Rendered fromOrthology-Beyond-GS.Rmdusingknitr::rmarkdown

Last update: 2025-04-30
Started: 2025-04-30

Performing Sequence Alignment in R
Downloading and installing MUSCLE and Clustal Omega | Performing alignment using the orthGS package | Performing alignment using the ape package | Performing alignment using the msa package | Performing alignment using the muscle package | Performing alignment integrating MUSCLE v5 in your R workflow
Rendered fromPerforming-Sequence-Alignment-in-R.Rmdusingknitr::rmarkdown

Last update: 2025-04-30
Started: 2025-04-30

Searching for GS Orthologs
Orthologs from crop in model plants and vice versa
Rendered fromSearching-for-Orthologous.Rmdusingknitr::rmarkdown

Last update: 2025-04-30
Started: 2025-04-30

Unraveling the Hiden Paralogs
Orthologs versus paralogs | Glutamine synthetase from conifers | Phylogenetic reconciliation | GS1a orthology network beyond conifers | References
Rendered fromUnraveling-the-Hiden-Paralogs.Rmdusingknitr::rmarkdown

Last update: 2025-04-30
Started: 2025-04-30