GrafGen

Classification of Helicobacter Pylori Genomes


Bioconductor version: Release (3.19)

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.

Author: William Wheeler [aut, cre], Difei Wang [aut], Isaac Zhao [aut], Yumi Jin [aut], Charles Rabkin [aut]

Maintainer: William Wheeler <wheelerb at imsweb.com>

Citation (from within R, enter citation("GrafGen")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("GrafGen")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GrafGen")
GrafGen: Classifying H. pylori genomes HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Genetics, GenomeAnnotation, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-2
Depends R (>= 4.3.0)
Imports stats, utils, graphics, ggplot2, plotly, zlibbioc, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang
System Requirements
URL
Bug Reports https://github.com/wheelerb/GrafGen/issues
See More
Suggests knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GrafGen_1.0.0.tar.gz
Windows Binary (x86_64) GrafGen_1.0.0.zip
macOS Binary (x86_64) GrafGen_1.0.0.tgz
macOS Binary (arm64) GrafGen_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GrafGen
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GrafGen
Bioc Package Browser https://code.bioconductor.org/browse/GrafGen/
Package Short Url https://bioconductor.org/packages/GrafGen/
Package Downloads Report Download Stats