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.

Version: 1.0.11
Depends: R (≥ 3.4.0)
Imports: rentrez (≥ 1.2.1), stringr (≥ 1.4.0), dplyr (≥ 0.8.0.1), httr (≥ 1.4.0), utils, curl (≥ 3.3)
Suggests: knitr, rmarkdown
Published: 2019-04-04
Author: Jose V. Die ORCID iD [aut, cre], Moamen M. Elmassry [ctb], Kimberly H. LeBlanc [ctb], Olaitan I. Awe [ctb], Allissa Dillman [ctb], Ben Busby [aut]
Maintainer: Jose V. Die <jose.die at uco.es>
BugReports: https://github.com/NCBI-Hackathons/GeneHummus/issues
License: MIT + file LICENSE
URL: https://github.com/NCBI-Hackathons/GeneHummus
NeedsCompilation: no
Materials: README
CRAN checks: geneHummus results

Downloads:

Reference manual: geneHummus.pdf
Package source: geneHummus_1.0.11.tar.gz
Windows binaries: r-devel: geneHummus_1.0.11.zip, r-release: geneHummus_1.0.11.zip, r-oldrel: geneHummus_1.0.11.zip
OS X binaries: r-release: geneHummus_1.0.11.tgz, r-oldrel: geneHummus_1.0.11.tgz
Old sources: geneHummus archive

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