Package: rhinotypeR 1.1.0

Martha Luka

rhinotypeR: Rhinovirus genotyping

"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.

Authors:Martha Luka [aut, cre], Ruth Nanjala [aut], Winfred Gatua [aut], Wafaa M. Rashed [aut], Olaitan Awe [aut]

rhinotypeR_1.1.0.tar.gz
rhinotypeR_1.1.0.zip(r-4.5)rhinotypeR_1.1.0.zip(r-4.4)
rhinotypeR_1.1.0.tgz(r-4.4-any)
rhinotypeR_1.1.0.tar.gz(r-4.5-noble)rhinotypeR_1.1.0.tar.gz(r-4.4-noble)
rhinotypeR_1.1.0.tgz(r-4.4-emscripten)
rhinotypeR.pdf |rhinotypeR.html
rhinotypeR/json (API)
NEWS

# Install 'rhinotypeR' in R:
install.packages('rhinotypeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/omicscodeathon/rhinotyper/issues

On BioConductor:rhinotypeR-1.1.0(bioc 3.21)rhinotypeR-1.0.0(bioc 3.20)

sequencinggeneticsphylogenetics

6.21 score 3 stars 2 scripts 10 exports 18 dependencies

Last updated 2 days agofrom:4fd8c8848c. Checks:OK: 1 NOTE: 3 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macWARNINGOct 31 2024

Exports:assignTypescountSNPsgetPrototypeSeqsoverallMeanDistancepairwiseDistancesplotAAplotDistancesplotFrequencyplotTreeSNPeek

Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc

Introduction to rhinotypeR

Rendered fromrhinotypeR.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-03
Started: 2024-07-16