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:
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')) |
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
Last updated 3 months agofrom:4fd8c8848c. Checks:1 OK, 4 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Dec 28 2024 |
| R-4.5-win | NOTE | Dec 31 2024 |
| R-4.5-linux | NOTE | Dec 28 2024 |
| R-4.4-win | NOTE | Dec 31 2024 |
| R-4.4-mac | NOTE | Dec 28 2024 |
Exports:assignTypescountSNPsgetPrototypeSeqsoverallMeanDistancepairwiseDistancesplotAAplotDistancesplotFrequencyplotTreeSNPeek
Dependencies:askpassBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assigns genotypes to input sequences | assignTypes |
| Counts single nucleotide polymorphisms | countSNPs |
| Download rhinovirus prototype strains | getPrototypeSeqs |
| Estimates the overall mean distance | overallMeanDistance |
| Estimates pairwise distances | pairwiseDistances |
| Visualize amino acid substitutions | plotAA |
| Visualizes pairwise genetic distances | plotDistances |
| Plots the frequency of assigned genotypes | plotFrequency |
| Plots a simple phylogenetic tree | plotTree |
| rhinotypeR: A Package for the genotyping of rhinoviruses using the VP4/2 region | rhinotypeR-package rhinotypeR |
| Visualize single nucleotide polymorphisms | SNPeek |