Package: orthGS 0.1.5
Elena Aledo
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:
orthGS_0.1.5.tar.gz
orthGS_0.1.5.zip(r-4.5)orthGS_0.1.5.zip(r-4.4)orthGS_0.1.5.zip(r-4.3)
orthGS_0.1.5.tgz(r-4.4-any)orthGS_0.1.5.tgz(r-4.3-any)
orthGS_0.1.5.tar.gz(r-4.5-noble)orthGS_0.1.5.tar.gz(r-4.4-noble)
orthGS_0.1.5.tgz(r-4.4-emscripten)orthGS_0.1.5.tgz(r-4.3-emscripten)
orthGS.pdf |orthGS.html✨
orthGS/json (API)
| # Install 'orthGS' in R: |
| install.packages('orthGS', repos = c('https://cranhaven.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cranhaven/cranhaven.r-universe.dev/issues
- A_selected - Adjacency Matrix for Orthology Graph
- AngGym - Angiosperms Gymnosperms
- agf - Angiosperms Gymnosperms Ferns
- sdf - Seed Plants and Ferns GS
- selected_tr - Ultrametric Rooted Seed Plants Tree
Last updated 2 days agofrom:ad9f47c0f4 (on package/orthGS). Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 24 2024 |
| R-4.5-win | OK | Nov 24 2024 |
| R-4.5-linux | OK | Nov 24 2024 |
| R-4.4-win | OK | Nov 24 2024 |
| R-4.4-mac | OK | Nov 24 2024 |
| R-4.3-win | OK | Nov 24 2024 |
| R-4.3-mac | OK | Nov 24 2024 |
Exports:coltipsgapless_msagetseqGSmadRootmapTreesmltreemsaorthGorthPspeciesGSsubsetGS
Dependencies:ade4apebio3dbitbit64bitopscastorcliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorsjsonlitelatticelifecyclemagrittrmapsMASSMatrixmnormtnaturalsortnlmenumDerivoptimParallelphangornphytoolspixmappkgconfigPlotToolsquadprogR.cacheR.methodsS3R.ooR.utilsrbibutilsRcppRcppArmadilloRcppEigenRCurlRdpackrlangRSpectrascatterplot3dsegmentedseqinrspTreeToolsvctrs
Searching for GS Orthologs
Rendered fromSearching_for_Orthologous.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2024-11-23
Started: 2024-11-23
Glutamine Synthetase from Conifers: Unraveling the Hidden Paralogs
Rendered fromUnraveling_the_hiden_paralogous.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2024-11-23
Started: 2024-11-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adjacency Matrix for Orthology Graph | A_selected |
| Angiosperms Gymnosperms Ferns | agf |
| Angiosperms Gymnosperms | AngGym |
| Colouring Tree Tips | coltips |
| Remove Gaps in a MSA | gapless_msa |
| Get the GS Sequence | getseqGS |
| Find The Root of a Phylogenetic Tree Using MAD Method | madRoot |
| Map Gene Tree into Species Tree | mapTrees |
| Build Up a ML Tree | mltree |
| Multiple Sequence Alignment | msa |
| Infer GS OrthoGroups Within a Set of Species | orthG |
| Search Orthologous of a Given Protein | orthP |
| Seed Plants and Ferns GS | sdf |
| Ultrametric Rooted Seed Plants Tree | selected_tr |
| Map Species Names | speciesGS |
| GS Proteins Report | subsetGS |
