Skip to contents

Changelog

glyenzy 0.9.0

Breaking changes

  • apply_enzyme() no longer accepts structure_level = "basic"; calls now error during argument validation. Use structure_level = "topological" to remove linkages while preserving concrete residue identities, and convert residues separately with glyrepr::convert_to_generic() when generic output is required.

New features

  • Built-in human enzyme rules now cover broader literature-supported acceptors with context-specific exclusions and requirements; Glc- or Gal-reducing structures without a represented carrier can be matched explicitly as free glycans or glycolipids. (#46)
  • Enzyme objects now carry broad glycan_type compatibility metadata for N-glycans, O-glycans, and glycolipids. Enzyme actions and biosynthesis searches use this metadata to avoid applying class-specific enzymes to incompatible glycan structures. (#45)
  • Human glycolipid coverage now includes UGCG, UGT8, B4GALT5, B4GALT6, and ST3GAL5, complete ganglioside rules for B3GALT4, B4GALNT1, and ST8SIA1, and corrected rules for ST6GALNAC3 and ST8SIA5. Glycolipid rules model carbohydrate headgroups with ceramide omitted. (#42)
  • New enzymes_from_rnaseq() selects built-in enzymes whose genes meet a configurable mean TPM threshold, using the GlycoMaple cutoff of TPM = 1 by default. (#43)
  • New product_substrate_ratio() calculates glycosyltransferase and sulfotransferase product-to-substrate motif quantification ratios from glycomics or site-specific glycoproteomics data, using lenient motif matching for partial or reduced structures. (#44)

Minor improvements and bug fixes

  • Built-in reaction rules now use reviewed acceptor and linkage specificity and include documented secondary activities for 15 glycosyltransferases. (#41)
  • apply_enzyme() with structure_level = "topological" now removes linkages while preserving residue identities; structure_level = "basic" is no longer supported.
  • find_enzyme() now batches product-motif matching across built-in enzyme rules, substantially improving performance while preserving special-case, substituent, requirement, and glycan-type handling. (#47)
  • path_biosynthesis() and trace_biosynthesis() now handle input vectors containing mixed generic and concrete residues element-wise and use lenient matching when needed.

glyenzy 0.8.1

Minor improvements and fixes

  • autoplot() now accepts the four glydraw 0.8.0 orientation values: "left", "right", "up", and "down".
  • Enzyme rules for MGAT4 and MGAT5 have been updated.
  • trace_biosynthesis() now infers max_steps from the largest target glycan when it is NULL, using its monosaccharide and substituent count plus 4 for N-glycans and minus 1 otherwise; explicit limits remain supported. (#40)
  • trace_biosynthesis() now returns a single-vertex target network when the target is already the selected starting glycan and no enzymatic steps are required. (#39)

glyenzy 0.8.0

New features

  • Biosynthesis functions now return typed glyenzy_biosynthesis_network objects that preserve their igraph interface and support collision-aware plot() and ggplot2::autoplot() layered DAG layouts with glycan nodes and labeled concrete or virtual enzyme edges. (#35, #36)
  • trace_biosynthesis() and trace_biosynthesis_virtual() now mark target glycans with a logical target vertex attribute; autoplot() highlights them by default in multi-target networks, with explicit control through highlight_target. (#37, #38)

glyenzy 0.7.0

Breaking changes

New features

  • Add first-class sulfotransferases (ST) with 12 human N- and O-glycan enzymes, sulfate-aware inference and biosynthesis, and virtual sulfation steps. (#20, #33)
  • path_biosynthesis() and trace_biosynthesis() gain max_virtual_steps to bridge a bounded number of unsupported, target-directed transitions before resuming concrete enzyme tracing; fallback edges are marked by is_virtual. (#32)
  • New trace_biosynthesis_virtual() and path_biosynthesis_virtual() build enzyme-agnostic networks by trimming targets backward; annotate_enzymes = TRUE adds exact rule-matched candidates in concrete_enzymes. (#22, #28, #30)
  • Add support for non-intact glycan structures by using lenient motif matching with a warning about reduced reliability. (#25)

Minor improvements and fixes

  • path_biosynthesis() and trace_biosynthesis() now scale better to large and multi-target searches by keeping intermediates as graphs, sharing prepared graph and rule work, vectorizing and batching frontier matching, caching graph products, pruning irreversible pre-MGAT2 decorations and occupied acceptor carbons, prioritizing inclusive targets, and using one multi-target reachability traversal. (#26, #29, #34)

glyenzy 0.6.3

Minor improvements and fixes

glyenzy 0.6.2

Minor improvements and fixes

  • Update built-in enzyme data and require glyrepr 0.13.0 or later for compatibility with refreshed glycan structure data (#24).

glyenzy 0.6.1

Minor improvements and fixes

  • Fix rules for MAN1A1, MAN1A2, and MAN1C1.

glyenzy 0.6.0

New features

Minor improvements and fixes

  • Fix enzyme printing without requiring users to attach glyrepr. (f0e42b2)

glyenzy 0.5.4

Minor improvements and fixes

glyenzy 0.5.3

Minor improvements and fixes

  • Update rules for FUT3, FUT4, FUT5, FUT6, FUT7, and FUT9. (2c6b28b)
  • Remove rules for B4GALT5, B4GALT6, and ST3GAL5 because these enzymes are exclusive for glycolipids. (798ea6f, 8dd30c8)
  • Update ST3GAL rules to reject Lewis antigen acceptors. (c969912)

glyenzy 0.5.2

Minor improvements and fixes

  • Fix rules for FUT3, FUT4, FUT5, FUT6, and FUT9. (5e7d657)

glyenzy 0.5.1

Minor improvements and fixes

  • Fix rules for FUT1, FUT2, and B3GALT5. (50f3d5d)

glyenzy 0.5.0

Breaking changes

New features

  • Add support for initiating enzymes including DPAGT1, FUT10, FUT11, POFUT1, POFUT2, POGLUT1, POGLUT2, POGLUT3, POMT1, POMT2, TMTC1, TMTC2, TMTC3, TMTC4, and GALNT1 through GALNT19. (#5)
  • Add support for N-glycan precursor synthesis enzymes (ALGs). (#6)
  • Add match_enzyme() to identify the residues added by a glycosyltransferase. (#3)
  • Add view_enzyme() to visualize residues added by an enzyme on a glycan cartoon. (#4)

Minor improvements and fixes

  • Fix the bug that find_enzyme didn’t support paucimannose glycans. (1c79a04)

glyenzy 0.4.3

Minor improvements and fixes

  • Update dependency strategy to use the r-universe repo.

glyenzy 0.4.2

Minor improvements and fixes

  • Update internal data to adapt to glyrepr 0.10.0.

glyenzy 0.4.1

Minor improvements and fixes

  • glyenzy now depends on the CRAN version of glyparse.

glyenzy 0.4.0

Breaking changes

  • Strengthen validation of the rejects field in enzyme rules: each reject must contain the acceptor motif.
  • Rework rejects handling in apply_enzyme() (and callers) to evaluate rejects per match rather than per glycan, improving accuracy for glycans with multiple acceptor matches.
  • Update built-in rules for MAN2A1, MAN2A2, MGAT3, MGAT4A, and MGAT4B to align with the new reject semantics.
  • Remove the now-redundant rejects_alignment field from enzyme_rule objects; acceptor_alignment is reused for reject checks.

New features

  • Add make_enzyme(), enabling programmatic construction of custom enzymes.

Minor improvements and fixes

glyenzy 0.3.2

Minor improvements and fixes

  • Fix errors in the rules of some enzymes, including B3GALT1, B3GALT2, and FUT8.
  • Fix a bug in progress bar of grow_glycans().

glyenzy 0.3.1

Minor improvements and fixes

  • glyenzy now depends on the CRAN version of glyrepr.

glyenzy 0.3.0

Breaking changes

  • Remove FUT10, as it belongs to the starting point of some O-Fuc glycans.

New features

  • Add many new enzymes, including FUT5, FUT6, ST3GAL5, ST6GALNAC5, ST6GALNAC6, ST8SIA1, ST8SIA5, ST8SIA6, B3GAT3, CHPF, CHPF2, CHSY1, CHSY3, EXT1, EXT2, HAS1, HAS2, HAS3, LARGE1, LARGE2, B3GLCT, A4GALT, ABO, B3GALT6, B4GALT6, GXYLT1, GXYLT2, LARGE1, LARGE2, XXYLT1, B3GALNT1, B4GALNT1, B4GALNT3, B4GALNT4, CSGALNACT1, CSGALNACT2, B3GNT5, B3GNT7, POMGNT1, POMGNT2, LFNG, MFNG, RFNG, EXLT1, EXLT2, EXLT3
  • Update the rules of some existing enzymes, including FUT1, FUT2, FUT3, FUT4, FUT7, FUT8, FUT9, ST3GAL2, ST3GAL3, ST3GAL4, ST6GALNAC1, ST6GALNAC3, ST8SIA2, ST8SIA3, ST8SIA4, B3GALT4, B3GALT5, B4GALT1, B4GALT4, B4GALT5, B4GALNT2, MGAT5B, B3GNT8, GCNT2, GCNT3, A4GNT, ST3GAL1
  • trace_biosynthesis() now supports many new glycan types, including O-Man, O-GlcNAc, O-Fuc, and O-Glc.

Minor improvements and fixes

  • path_biosynthesis() and trace_biosynthesis() has been optimized for large glycans.
  • All functions explicitly check if the input glycans are concrete (e.g. “Glc”, “GalNAc”) and raise errors with helpful messages if not.

glyenzy 0.2.3

Minor improvements and bug fixes

  • Updated dependency on glymotif (>= 0.10.0) to ensure compatibility with recent changes in package igraph v2.2.0.

glyenzy 0.2.2

Minor improvements and bug fixes

  • Fix bugs introduced by the breaking changes in glymotif v0.7.0 and glyrepr v0.7.0.

glyenzy 0.2.1

Minor improvements and bug fixes

  • Update dependencies to depend on release versions of glycoverse packages.

glyenzy 0.2.0

Breaking changes

New features

  • trace_biosynthesis() now supports multiple target glycans. The resulting graph contains all given target glycans and intermediate glycans.

Minor improvements and fixes

  • Update documentations of path_biosynthesis() and trace_biosynthesis() to include some important notes.
  • Fix bugs in path_biosynthesis() and trace_biosynthesis() that glycan structure strings other than IUPAC-condensed format cannot be parsed.
  • Add checks in all functions to ensure that the input glycans have intact linkages and no substituents, and raise errors with helpful messages if not.
  • Refactor apply_enzyme() to stop using internal glymotif functions to avoid fragile dependency.

glyenzy 0.1.1

Minor improvements and fixes

  • Fix bugs introduced by the breaking changes in glyrepr v0.7.0.

glyenzy 0.1.0

First release of glyenzy!