Package: geneHummus 1.0.11
geneHummus: A Pipeline to Define Gene Families in Legumes and Beyond
A pipeline with high specificity and sensitivity in extracting proteins from the RefSeq database (National Center for Biotechnology Information). Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family. The pipelines implements an automatic approach for the identification of gene families based on the conserved domains that specifically define that family. See Die et al. (2018) <doi:10.1101/436659> for more information and examples.
Authors:
geneHummus_1.0.11.tar.gz
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geneHummus.pdf |geneHummus.html✨
geneHummus/json (API)
# Install 'geneHummus' in R: |
install.packages('geneHummus', repos = c('https://ncbi-hackathons.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ncbi-hackathons/genehummus/issues
- legumesIds - NCBI taxonomy ids for the legume family
- my_legumes - ARF proteins per legume specie
Last updated 4 years agofrom:1fb3618176. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 12 2024 |
R-4.5-win | WARNING | Nov 12 2024 |
R-4.5-linux | WARNING | Nov 12 2024 |
R-4.4-win | WARNING | Nov 12 2024 |
R-4.4-mac | WARNING | Nov 12 2024 |
R-4.3-win | WARNING | Nov 12 2024 |
R-4.3-mac | WARNING | Nov 12 2024 |
Exports:accessions_by_sppaccessions_from_sppfilterArch_idsgetAccessionsgetArch_idsgetArch_labelsgetProteins_from_tax_ids
Dependencies:askpassclicurldplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rentrezrlangstringistringrsystibbletidyselectutf8vctrswithrXML