GrafGen

This is the released version of GrafGen; for the devel version, see GrafGen.

Classification of Helicobacter Pylori Genomes

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DOI: 10.18129/B9.bioc.GrafGen

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Genetics, GenomeAnnotation, Software

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License GPL-2

Depends R (>= 4.3.0)

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

System Requirements

URL

Bug Reports https://github.com/wheelerb/GrafGen/issues

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

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Package Archives

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

Source Package GrafGen_1.6.0.tar.gz

Windows Binary (x86_64) GrafGen_1.6.0.zip

macOS Binary (x86_64) GrafGen_1.6.0.tgz

macOS Binary (arm64) GrafGen_1.6.0.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/

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