Background | Installing the package | Load rhinotypeR | Input expectations | Option A: Align externally | Option B: Align in R | Assign types | Plot results | Distances and summaries | SNP and amino acid views | Quality and troubleshooting | Conclusion | Session info
Package: rhinotypeR 1.7.3
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_1.7.3.tar.gz
rhinotypeR_1.7.3.zip(r-4.7)rhinotypeR_1.7.3.zip(r-4.6)rhinotypeR_1.7.3.zip(r-4.5)
rhinotypeR_1.7.3.tgz(r-4.6-any)rhinotypeR_1.7.3.tgz(r-4.5-any)
rhinotypeR_1.7.3.tar.gz(r-4.7-any)rhinotypeR_1.7.3.tar.gz(r-4.6-any)
rhinotypeR_1.7.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rhinotypeR/json (API)
| # 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
Datasets:
- rhinovirusPrototypesVP4 - Rhinovirus VP4/2 prototype references
- rhinovirusVP4 - Example VP4/2 alignment
On BioConductor:rhinotypeR-1.7.0(bioc 3.24)rhinotypeR-1.6.0(bioc 3.23)
sequencinggeneticsphylogeneticsvisualizationmultiplesequencealignmentmultiplecomparison
Last updated from:94000ac0b0. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 189 | ||
| linux-devel-x86_64 | NOTE | 449 | ||
| source / vignettes | OK | 200 | ||
| linux-release-x86_64 | NOTE | 497 | ||
| macos-release-arm64 | NOTE | 490 | ||
| macos-oldrel-arm64 | NOTE | 429 | ||
| windows-devel | NOTE | 337 | ||
| windows-release | NOTE | 347 | ||
| windows-oldrel | NOTE | 362 | ||
| wasm-release | OK | 162 |
Exports:alignToRefsassignTypescountSNPsgetPrototypeSeqsoverallMeanDistancepairwiseDistancesplotAAplotDistancesplotFrequencyplotTreeSNPeek
Dependencies:ade4apeBiocGenericsBiostringsclicodetoolscpp11crayondigestdoParalleldplyrforeachgenericsGenomicRangesglueIRangesiteratorslatticelifecyclemagrittrMASSmsaMSA2distMultipleAlignmentnlmepillarpixmappkgconfigpurrrpwalignR6RcppRcppArmadilloRcppThreadrlangS4VectorssegmentedSeqinfoseqinrspstringistringrtibbletidyrtidyselectutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Align user sequences to packaged rhinovirus prototype references | alignToRefs |
| Assign rhinovirus genotypes based on pairwise distances to prototype strains | assignTypes |
| Count pairwise SNPs between aligned DNA sequences | countSNPs |
| Download rhinovirus prototype strains (optional) | getPrototypeSeqs |
| Overall Mean Pairwise Distance | overallMeanDistance |
| Compute pairwise genetic distances between aligned DNA sequences | pairwiseDistances |
| Visualize amino acid differences against a reference (fast zoom & highlighting) | plotAA |
| Plot Pairwise Distance Heatmap | plotDistances |
| Plot Frequency of Assigned Rhinovirus Types | plotFrequency |
| Plot a Phylogenetic Tree from a Distance Matrix | plotTree |
| rhinotypeR: VP4/2-based genotyping and visualization for human rhinoviruses | rhinotypeR-package rhinotypeR |
| Rhinovirus VP4/2 prototype references (DNAStringSet) | rhinovirusPrototypesVP4 |
| Example VP4/2 alignment (DNAStringSet) | rhinovirusVP4 |
| Visualize SNP differences against a reference (fast zoom & highlighting) | SNPeek |