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
geneHummus_1.0.11.zip(r-4.5)geneHummus_1.0.11.zip(r-4.4)geneHummus_1.0.11.zip(r-4.3)
geneHummus_1.0.11.tgz(r-4.4-any)geneHummus_1.0.11.tgz(r-4.3-any)
geneHummus_1.0.11.tar.gz(r-4.5-noble)geneHummus_1.0.11.tar.gz(r-4.4-noble)
geneHummus_1.0.11.tgz(r-4.4-emscripten)geneHummus_1.0.11.tgz(r-4.3-emscripten)
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'))

Peer review:

Bug tracker:https://github.com/ncbi-hackathons/genehummus/issues

Datasets:

On CRAN:

4.15 score 7 stars 3 scripts 187 downloads 2 mentions 7 exports 27 dependencies

Last updated 4 years agofrom:1fb3618176. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winWARNINGNov 12 2024
R-4.5-linuxWARNINGNov 12 2024
R-4.4-winWARNINGNov 12 2024
R-4.4-macWARNINGNov 12 2024
R-4.3-winWARNINGNov 12 2024
R-4.3-macWARNINGNov 12 2024

Exports:accessions_by_sppaccessions_from_sppfilterArch_idsgetAccessionsgetArch_idsgetArch_labelsgetProteins_from_tax_ids

Dependencies:askpassclicurldplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rentrezrlangstringistringrsystibbletidyselectutf8vctrswithrXML