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Changelog

Source: NEWS.md

glyrepr (development version)

New features

  • Update the monosaccharides table:
    • Add generic monosaccharides to Ara, Lyx, Xyl, Rib, Api, Neu, Kdn, Pse, Leg, Aci, 4eLeg, Bac, LDmanHep, DDmanHep, Kdo, Dha, MurNAc, MurNGc, Mur, Fru, Tag, Sor, Psi.
    • Rename “Pent” to “Pen”.
    • Delete “Sia” from the table.
  • Update the logic of monosaccharide type determination for glycan compositions and glycan structures, considering some special monosaccharides have the same name for both generic and concrete types (e.g. “Neu”, “Mur”). The new rules:
    • Mixed monosaccharides are still not allowed.
    • If all residues besides the special monosaccharides are of the same type, it will be determined as the glycan monosaccharide type.
    • If all residues are special monosaccharides, it will be determined as “concrete”.
  • count_mono() now supports counting substituents, with a new argument include_subs.

Minor improvements and bug fixes

glyrepr 0.8.0

CRAN release: 2025-11-09

Breaking changes

  • Remove normalize_substituents(). This function does not help outside of glyrepr so we make it an internal function.
  • glycan_composition() cannot accept empty integer vectors now. Therefore, glycan_composition(integer(0)) is not valid anymore.
  • glycan_composition() now checks input types more strictly.
  • as_glycan_composition() handles NA values and empty strings (““) more strictly. Now an error will be raised if NA values or empty strings are passed instead of dropping them silently. This update makes as_glycan_composition() size-stable and consistent with as_glycan_structure().

New features

  • Add get_structure_level() to get the structure resolution levels of a glycan structure vector.
  • as_glycan_composition() now supports simple composition strings like “H5N2”, “H5N4F1S2”, “H5N4A1G1”, etc.
  • count_mono() now returns total number of monosaccharides when mono is NULL.
  • has_linkages() now has a strict parameter to control the strictness of the check.

Minor improvements and bug fixes

glyrepr 0.7.5

CRAN release: 2025-10-29

Minor improvements and bug fixes

  • IUPAC sequence generation is deterministic now for tie branches.
  • Glycan structures are now truncated when printed to console as a column in a tibble.
  • Glycan compositions are now colored when printed to console as a column in a tibble.

glyrepr 0.7.4

CRAN release: 2025-09-23

Minor improvements and bug fixes

  • Update package title and description.
  • Remove parallel examples in smap().

glyrepr 0.7.3

Minor improvements and bug fixes

  • Fix some typos in the documentation.
  • Add examples to some functions.
  • Prepare for release on CRAN.

glyrepr 0.7.2

Minor improvements and bug fixes

  • Fix the bug that structure_to_iupac() returns incorrect sequences with incorrect backbone or branch order.

glyrepr 0.7.1

Minor improvements and bug fixes

  • Fix the bug that smap2(), spmap(), and related functions return unexpected results when the input y is a list.
  • Improve the documentation of glycan_structure(), including the new behavior of vertex and edge order introduced in 0.7.0.

glyrepr 0.7.0

Breaking changes

  • convert_mono_type() is now replaced by convert_to_generic(). convert_mono_type() was created when three monosaccharide types existed: “concrete”, “generic”, and “simple”. When “simple” was removed, the old convert_mono_type() seems redundant, as the only valid conversion is from “concrete” to “generic” now. Therefore, we remove this function now and add a more straightforward convert_to_generic().
  • get_structure_graphs() is redesigned.
    • The i parameter is removed, as indexing can be done manually on the input glyrepr_structure vector or on the returned list easily.
    • Add a return_list parameter to control the return type. This parameter makes this function “type-stable”.
  • glycan_structure() and as_glycan_structure() now reorder the underlying graphs to be in line with the IUPAC-style sequence. For example, the vertex order of “Gal(b1-3)[GlcNAc(b1-6)]GalNAc(b1-” is always 1. Gal, 2. GlcNAc, 3. GalNAc, and edges b1-3, b1-6, no matter what the original graphs are. Users can assign the indices of vertices and edges easily by printing the structure to console. This update makes glymotif::match_motif() more meaningful.

New features

  • glyrepr_structure has colors now in tibbles when printed to console.

Minor improvements and bug fixes

  • Fix the bug that monosaccharides with substituents are not colored when a glycan_structure() is printed in the console. For example, the “Neu5Ac” part in “Neu5Ac9Ac(a2-” was printed in black. Now it is printed in purple, while the “9Ac” part remains in black.
  • Fix the bug that Neu5Ac and Neu5Gc with substituents at position 2, 3, or 4 could not be correctly parsed. Now, complex patterns like “Neu4Ac5Ac9Ac” can be properly handled, into a “Neu5Ac” monosaccharide with “4Ac,9Ac” as substituents.

glyrepr 0.6.1

Minor improvements and bug fixes

glyrepr 0.6.0

Breaking changes

  • Remove the “alditol” attribute from glycan_structure() objects. This information is rarely used in glycomics and glycoproteomics data analysis. It is removed according to the razor principle.
  • as_glycan_structure() now doesn’t allow the input IUPAC-condensed strings to omit the anomer information. Previously, something like “Glc(a1-3)GlcNAc” is valid. as_glycan_structure() assumed that the core “GlcNAc” has a “?1-” anomer and added it automatically. The problem is that this behavior was not easily awared by users and might cause confusion. Again, less is more, so we remove it.

glyrepr 0.5.2

Minor improvements and bug fixes

  • Fix some error message format errors.
  • Update the abbreviated type name of glyrepr_structure from structure to struct.

glyrepr 0.5.0

Major changes

  • Glycan structures now support multiple substituents on a single monosaccharide. Substituents are stored as comma-separated strings internally and concatenated in IUPAC format for display.

  • Glycan compositions now support substituents. The glycan_composition class can now represent and count substituents alongside monosaccharides.