GrafGen
This is the development version of GrafGen; for the stable release version, see GrafGen.
Classification of Helicobacter Pylori Genomes
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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 |
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_1.9.0.tar.gz |
| Windows Binary (x86_64) | GrafGen_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | GrafGen_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | GrafGen_1.9.0.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 |