Package: REFT 0.1.4
Guozhen Gao
REFT: Root Exudate Feature Toolkit
Provides tools for molecule-oriented and reaction-centred analysis of root exudate datasets. It supports structural matching based on 'PubChem', calculation of molecular descriptors, and inference of candidate microbe-associated metabolic reactions using Kyoto Encyclopedia of Genes and Genomes ('KEGG') identifiers and Enzyme Commission ('EC') numbers. For background on these databases, see Kanehisa et al. (2023) <doi:10.1093/nar/gkac963> and Kim et al. (2023) <doi:10.1093/nar/gkac956>.
Authors:
REFT_0.1.4.tar.gz
REFT_0.1.4.tar.gz(r-4.7-any)REFT_0.1.4.tar.gz(r-4.6-any)
REFT_0.1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
REFT/json (API)
| # Install 'REFT' in R: |
| install.packages('REFT', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gaoguozhen1/reft/issues
Last updated from:1df3cfbde4. Checks:2 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 155 | ||
| source / vignettes | OK | 175 | ||
| linux-release-x86_64 | NOTE | 169 | ||
| wasm-release | OK | 117 |
Exports:reft_calc_descriptorsreft_kegg_microbe_runreft_match_smilesreft_runreft_run_simple
Dependencies:askpassbase64enccellrangerclicpp11crayoncurldata.treedplyrgenericsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6readxlrematchrlangrvestselectrstringistringrsystibbletidyselectutf8vctrswebchemwithrwritexlxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| REFT: Root Exudate Feature Toolkit | REFT |
| Calculate six molecular descriptors | reft_calc_descriptors |
| Run KEGG microbe-EC-reaction search workflow | reft_kegg_microbe_run |
| Match SMILES from PubChem | reft_match_smiles |
| Run the full REFT workflow | reft_run |
| Run REFT with default column names | reft_run_simple |
