rhinotypeR

This is the development version of rhinotypeR; for the stable release version, see rhinotypeR.

Rhinovirus genotyping

Bioconductor version: Development (3.21)

"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.

Author: Martha Luka [aut, cre] (ORCID: ), Ruth Nanjala [aut], Winfred Gatua [aut], Wafaa M. Rashed [aut], Olaitan Awe [aut]

Maintainer: Martha Luka <marthaluka20 at gmail.com>

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

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("rhinotypeR")

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("rhinotypeR")

Introduction to rhinotypeR	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Genetics, Phylogenetics, Sequencing, Software
Version	1.1.0
In Bioconductor since	BioC 3.20 (R-4.4) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.4.0)
Imports	Biostrings
System Requirements
URL	https://github.com/omicscodeathon/rhinotypeR
Bug Reports	https://github.com/omicscodeathon/rhinotypeR/issues

Suggests	knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0)
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	rhinotypeR_1.1.0.tar.gz
Windows Binary (x86_64)	rhinotypeR_1.1.0.zip (64-bit only)
macOS Binary (x86_64)	rhinotypeR_1.1.0.tgz
macOS Binary (arm64)	rhinotypeR_1.1.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rhinotypeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rhinotypeR
Bioc Package Browser	https://code.bioconductor.org/browse/rhinotypeR/
Package Short Url	https://bioconductor.org/packages/rhinotypeR/
Package Downloads Report	Download Stats