Issues

• Calibrate SLP/mRNA trajectories with target-bearing lymph fragments and APC surface pMHC

  openvax/mhctools#549 · Filter by author iskandr opened on Oct 9, 2026

• Native MixMHCpred sequence-alignment reference times out during full local suite

  openvax/mhctools#547 · Filter by author iskandr opened on Oct 9, 2026
  2

• Replace typechecks with isinstance checks and type annotations

  openvax/mhctools#535 · Filter by author iskandr opened on Oct 7, 2026

• Use consistent dashed red bond markers in the processing atlas

  openvax/mhctools#534 · Filter by author iskandr opened on Oct 7, 2026

• Refresh fresh-report availability audit for released PhageScout profiles

  openvax/mhctools#533 · Filter by author iskandr opened on Oct 7, 2026

• Recover released PhageScout classifier preprocessing for faithful new-sequence inference

  openvax/mhctools#521 · Filter by author iskandr opened on Oct 6, 2026
  1

• Add distinct human ELANE and PRTN3 extended-recognition evidence and independent inflammatory-protease benchmarks

  openvax/mhctools#519 · Filter by author iskandr opened on Oct 6, 2026

• Add human plasma kallikrein KLKB1 recognition evidence separately from tissue KLKs

  openvax/mhctools#518 · Filter by author iskandr opened on Oct 6, 2026

• Add assay-scoped human plasmin extended-recognition evidence without treating Lys/Arg as sufficient

  openvax/mhctools#517 · Filter by author iskandr opened on Oct 6, 2026

• Add extended human thrombin recognition rules with source-backed cooperative motifs

  openvax/mhctools#516 · Filter by author iskandr opened on Oct 6, 2026

• Add pH-scoped human legumain/AEP recognition evidence and observed cleavage sites

  openvax/mhctools#515 · Filter by author iskandr opened on Oct 6, 2026

• Add assay-scoped CatL sequence-recognition evidence from PICS/DIPPS and peptide-library measurements

  openvax/mhctools#514 · Filter by author iskandr opened on Oct 6, 2026

• Include skipped-test reasons in default test.sh logs

  openvax/mhctools#509 · Filter by author iskandr opened on Oct 6, 2026
  1

• Add CleaveNet MMP substrate predictions with native endpoint and assay provenance

  openvax/mhctools#476 · Filter by author iskandr opened on Sep 30, 2026
  1

• Add assay-scoped cathepsin and AEP coverage for APC cleavage assessments

  openvax/mhctools#470 · Filter by author iskandr opened on Sep 29, 2026
  2

• Make the SMM subset audit independent of zlib compression differences

  openvax/mhctools#465 · Filter by author iskandr opened on Sep 28, 2026

• Allow optional predictor selection when embedding add_mhc_args in cache-only workflows

  openvax/mhctools#444 · Filter by author iskandr opened on Sep 21, 2026

• Remove signature-mirror and attribute-presence tests that never call the API

  openvax/mhctools#443 · Filter by author iskandr opened on Sep 21, 2026

• Unreferenced code: IEDB method lists, a duplicate flank helper, elution_score, an unreachable mhcflurry import guard

  openvax/mhctools#353 · Filter by author iskandr opened on Sep 14, 2026

• Remaining round-3 review nitpicks: test factory dedup, alternate --compartment CLI design

  openvax/mhctools#337 · Filter by author iskandr opened on Sep 14, 2026

• Minor: cleavage_models()/get_cleavage_model() do repeated linear work with no caching

  openvax/mhctools#336 · Filter by author iskandr opened on Sep 11, 2026

• Curate remaining intracellular peptidases and settle the THOP1 epitope-substrate disagreement

  openvax/mhctools#334 · Filter by author iskandr opened on Sep 10, 2026

• Resolve conflicting IRAP resistant-precursor sequence in Georgiadou 2010 before benchmarking

  openvax/mhctools#332 · Filter by author iskandr opened on Sep 10, 2026

• Validate organ-exposure comparisons without conflating tissue signal, intact peptide and cell-specific delivery

  openvax/mhctools#307 · Filter by author iskandr opened on Sep 9, 2026

• Assess draining-lymph-node exposure and injection-site compartments as distinct vaccine-relevant endpoints

  openvax/mhctools#306 · Filter by author iskandr opened on Sep 9, 2026