NEWS
glydb 0.7.2
- Installation now uses the released
glyrepr (>= 1.1.0) and glyparse (>= 0.8.1) packages instead of development versions.
glydb 0.7.1
Minor improvements and bug fixes
- Update bundled data from GlyGen 2.11.1 to 2.12.1, increasing coverage from 49,019 to 49,728 glycan structures (709 additional accessions, with all previous accessions retained). Regenerate internal composition, structure, and GlyTouCan lookup indexes. (#18)
- Incorporate upstream WURCS revisions affecting 77 existing structures, with their monosaccharide compositions unchanged. For reproducible analyses, pin the glydb package version and record the bundled GlyGen data version.
glydb 0.7.0
Breaking changes
glydb_structures() now accepts only "intact" and "topological" structure levels; use mono_type = "generic" with structure_level = "topological" instead of the removed "basic" level.glytoucan_to_struc() no longer falls back to the online GlyGen API. Accessions without a bundled glydb_data match now return NA. (#16)
New features
glydb_data now includes 49,019 GlyGen glycan structures parsed from WURCS sequences, substantially expanding bundled GlyTouCan coverage. (#15)glydb_compositions() and glydb_structures() now preserve their confidence attributes through vector operations. When identical glycans with different confidence values are combined, the maximum value is used. (#14)glydb_structures() gains an independent mono_type argument for retrieving concrete or generic monosaccharide structures. For generic topological structures, use mono_type = "generic" with structure_level = "topological" instead of the removed "basic" level.- New
struc_to_glytoucan() maps glycan structures to bundled GlyTouCan accessions. (#16)
glydb 0.6.0
New features
glydb_data now contains 19,436 GlyGen glycan structures, including non-intact glycans (#9).
Minor improvements and bug fixes
- Bundled
glydb_data and internal structure indexes are regenerated for compatibility with glyrepr 0.13.0 (#13).
glytoucan_to_struc() now looks up accessions from glydb_data first and only falls back to the online GlyGen API for missing accessions. (#10)glycan_type values now use GlyGen classifications, including HMO, GSL, GAG, GPI, and reducing-end O-linked subtypes (#12).
glydb 0.5.0
New features
- Add
glytoucan_to_struc() to fetch GlyTouCan accessions from the GlyGen API and parse returned IUPAC strings into glycan structures (#7).
Minor improvements and bug fixes
- Update internal data to use the GlyTouCan v2.11.1 release.
glydb 0.4.1
Minor improvements and bug fixes
- Update documentation to correctly reflect data version.
glydb 0.4.0
New features
- Add a
mono_range parameter to glydb_compositions() and glydb_structures().
glydb_compositions() and glydb_structures() now return a vector with a confidence attribute, readily used by the glyanno package to rank the results.glydb_data now has new confidence column.
glydb 0.3.3
Minor improvements and bug fixes
- Update internal data to use GlyGen Datasets v2.10.1.
glydb 0.3.2
Minor improvements and bug fixes
glydb 0.3.1
Minor improvements and bug fixes
- glydb now depends on CRAN version of glyrepr 0.9.0.
glydb 0.3.0
New features
- Add a
glycan_type column to glydb_data. Can be "N", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc".
- Add a
glycan_type parameter to glydb_compositions() and glydb_structures().
glydb 0.2.1
Minor improvements and bug fixes
- Fix the bug that
glydb_species() fails when the package is used via glydb::fun and not attached with library(glydb).
glydb 0.2.0
Breaking changes
- Remove the
topology_glycans dataset.
- Rename the
fully_determined_glycans dataset to glydb_data.
New features
- Add
glydb_species() to get the species names from glydb_data.
- Add
glydb_compositions() to get the glycan compositions from glydb_data with different monosaccharide types.
- Add
glydb_structures() to get the glycan structures from glydb_data with different structure levels.
Minor improvements and bug fixes
- Update the documentation of
glydb_data to explain the duplicate glycan structures in the dataset.
glydb 0.1.1
Minor improvements and bug fixes
- Update the
topology_glycans dataset to remove some duplicates.
glydb 0.1.0