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
DOI:	10.32614/CRAN.package.geneHummus
Author:	Jose V. Die [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

Documentation:

Reference manual:

geneHummus.pdf

Downloads:

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
macOS binaries:	r-release (arm64): geneHummus_1.0.11.tgz, r-oldrel (arm64): geneHummus_1.0.11.tgz, r-release (x86_64): geneHummus_1.0.11.tgz, r-oldrel (x86_64): geneHummus_1.0.11.tgz
Old sources:	geneHummus archive

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