Package: geneHummus 1.0.11

Jose V. Die

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:Jose V. Die [aut, cre], Moamen M. Elmassry [ctb], Kimberly H. LeBlanc [ctb], Olaitan I. Awe [ctb], Allissa Dillman [ctb], Ben Busby [aut]

geneHummus_1.0.11.tar.gz
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geneHummus_1.0.11.tgz(r-4.5-any)geneHummus_1.0.11.tgz(r-4.4-any)geneHummus_1.0.11.tgz(r-4.3-any)
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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

Datasets:

On CRAN:

Conda:

4.20 score 8 stars 3 scripts 191 downloads 2 mentions 7 exports 27 dependencies

Last updated 5 years agofrom:1fb3618176. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 12 2025
R-4.5-winWARNINGMar 12 2025
R-4.5-macWARNINGMar 12 2025
R-4.5-linuxWARNINGMar 12 2025
R-4.4-winWARNINGMar 12 2025
R-4.4-macWARNINGMar 12 2025
R-4.4-linuxWARNINGMar 12 2025
R-4.3-winWARNINGMar 12 2025
R-4.3-macWARNINGMar 12 2025

Exports:accessions_by_sppaccessions_from_sppfilterArch_idsgetAccessionsgetArch_idsgetArch_labelsgetProteins_from_tax_ids

Dependencies:askpassclicurldplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rentrezrlangstringistringrsystibbletidyselectutf8vctrswithrXML