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) for more information and examples.

title: "README" author: "Jose V Die" date: "28/2/2019" output: html_document

geneHummus

An Automated Pipeline to Study Plant Gene Families based on Protein Domain Organization using Auxin Response Factors in chickpea and other Legumes as an Example. The pipeline is convenient if you are interested in plant gene families characterization, or you'd like to perform some downstream analysis such as phylogenetic construction or gene expression profiling, to name a few examples.

Accessing the package

A stable version of this package is available on CRAN and can be installed directly from there:

install.packages("geneHummus")

The lastest development version of the package can also be loaded directly from GitHub using the devtools package:

library(devtools)
install_github("NCBI-Hackathons/GeneHummus")
library(GeneHummus)

Publication

Die JV, Elmassry MM, Leblanc KH, Awe OI, Dillman A, Busby B (2018) GeneHummus: A pipeline to define gene families and their expression in legumes and beyond, bioRxiv 436659; doi: https://doi.org/10.1101/436659