rhinotypeR
This is the released version of rhinotypeR; for the devel version, see rhinotypeR.
Rhinovirus genotyping
Bioconductor version: Release (3.23)
"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] 
, Ruth Nanjala [aut], Winfred Gatua [aut], Wafaa M. Rashed [aut], Olaitan Awe [aut]
Maintainer: Martha Luka <marthaluka20 at gmail.com>
citation("rhinotypeR")):Martha Luka, Ruth Nanjala, Winfred Gatua, Wafaa M. Rashed, Olaitan Awe. rhinotypeR: Rhinovirus genotyping. doi:10.18129/B9.bioc.rhinotypeR, R package version 1.6.0, https://bioconductor.org/packages/rhinotypeR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Genetics, MultipleComparison, MultipleSequenceAlignment, Phylogenetics, Sequencing, Software, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | Biostrings, methods, MSA2dist, msa |
| System Requirements | |
| URL | https://github.com/omicscodeathon/rhinotypeR |
| Bug Reports | https://github.com/omicscodeathon/rhinotypeR/issues |
See More
| 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rhinotypeR_1.6.0.tar.gz |
| Windows Binary (x86_64) | rhinotypeR_1.6.0.zip |
| macOS Binary (big-sur-x86_64) | rhinotypeR_1.6.0.tgz |
| macOS Binary (sonoma-arm64) | rhinotypeR_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rhinotypeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rhinotypeR |
| Package Short Url | https://bioconductor.org/packages/rhinotypeR/ |
| Package Downloads Report | Download Stats |