GrafGen
This is the development version of GrafGen; for the stable release version, see GrafGen.
Classification of Helicobacter Pylori Genomes
Bioconductor version: Development (3.21)
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("GrafGen")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Genetics, GenomeAnnotation, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | GrafGen_1.3.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GrafGen |
| Source Repository (Developer Access) | git clone [email protected]:packages/GrafGen |
| Bioc Package Browser | https://code.bioconductor.org/browse/GrafGen/ |
| Package Short Url | https://bioconductor.org/packages/GrafGen/ |
| Package Downloads Report | Download Stats |