GrafGen

Classification of Helicobacter Pylori Genomes

Bioconductor version: 3.23 · Package version: 1.8.0

To classify Helicobacter pylori genomes according to genetic distance from nine reference populations. The nine reference populations are hpgpAfrica, hpgpAfrica-distant, hpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope, hpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex populations are Africa, Europe and Asia.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GrafGen")

Details

Maintainer	William Wheeler <wheelerb@imsweb.com>
Author	William Wheeler [aut, cre], Difei Wang [aut], Isaac Zhao [aut], Yumi Jin [aut], Charles Rabkin [aut]
License	GPL-2
Bug Reports	https://github.com/wheelerb/GrafGen/issues
Downloads rank	190
Source branch	RELEASE_3_23
biocViews	Classification, Genetics, GenomeAnnotation, Software

Documentation

GrafGen: Classifying Subpopulations of H. pylori Genomes

Download

Source package

Dependencies

Depends: R (>= 4.3.0)

Imports: stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang

Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools