NEWS
rhinotypeR 2026-07-03 (2026-07-03)
Fixed
- Updated handling of MultipleAlignment classes for compatibility with
Bioconductor 3.24 (Added MultipleAlignment to Depends to ensure compatibility with msa
alignment objects).
rhinotypeR 2026-06-16 (2026-06-16)
Fixed
- Updated handling of MultipleAlignment classes for compatibility with
Bioconductor 3.24.
- Fixed alignment-related test failures under R CMD check.
rhinotypeR 2026-06-09 (2026-06-09)
Fixed
- Updated imports of DNAMultipleAlignment and related functionality following
changes in Bioconductor 3.24, where multiple-alignment classes and methods
were moved from Biostrings to MultipleAlignment.
rhinotypeR 2025-10-21 (2025-10-21)
Fixed
- Example and test errors related to internal helpers (compareAndColorSequences(),
compute_cache()) now handled safely using \dontrun{} and updated documentation.
- Removed outdated License stub issue and corrected DESCRIPTION metadata formatting.
- Corrected internal tests referencing deprecated testthat::local_null_device().
Improved
- CountSNPs() re-implementation: directly computes pairwise SNP counts without
relying on model-based rounding (e.g., from MSA2dist). No rounding artifacts
rhinotypeR 2025-10-01 (2025-10-01)
Added
- New function:
alignToRefs(), which aligns user sequences to the packaged
rhinovirus prototype references using msa::msa() (ClustalW, ClustalOmega, or MUSCLE),
with an option to trim alignments to the non-gap span of a chosen reference.
Improved
- SNPeek() and plotAA(): now support zooming to specific genomic regions
and highlighting individual sequences of interest.
- assignTypes(): now reports the genetic distance to the nearest prototype
even when the query is
"unassigned".
- Distance calculation: switched to using MSA2dist for pairwise distance
computation. This provides broader model support — access to all substitution
models in ape::dist.dna, in addition to the
"IUPAC" model.
- Data access: prototype and example datasets are now exported as packaged
objects (
rhinovirusVP4, rhinovirusPrototypesVP4) instead of being accessed
via system.file(), simplifying workflows.
- Improved documentation:
- Improved explanations and runnable examples added where feasible.
- Visualization functions return results invisibly to avoid console clutter,
while still allowing advanced users to capture outputs.
- Code style and formatting improved (e.g.,consistent internal helpers).
rhinotypeR 0.1.0
- First public release of rhinotypeR.
- Implements VP4/2-based rhinovirus genotyping workflow.
- Provides bundled prototype reference sequences and example datasets.