Issues

• Preserve dated Ensembl releases in CTA annotation provenance

  openvax/vaxrank#662 · Filter by author iskandr opened on Oct 20, 2026

• Raise minimum supported pandas to 3.0

  openvax/vaxrank#659 · Filter by author iskandr opened on Oct 20, 2026

• Test HCC1395 and COLO829 matched-normal RNA-supported somatic proteins

  openvax/vaxrank#658 · Filter by author iskandr opened on Oct 20, 2026
  1

• Cover canine WLOS_0001 RNA-supported somatic proteins in Vaxrank

  openvax/vaxrank#657 · Filter by author iskandr opened on Oct 20, 2026
  2

• Test sample-derived SiHa HPV16 E7 provenance through Vaxrank

  openvax/vaxrank#656 · Filter by author iskandr opened on Oct 20, 2026

• Transient SSH read after release-lock cleanup reports a completed deploy as failed

  openvax/vaxrank#650 · Filter by author iskandr opened on Oct 19, 2026

• Index host-reference peptide queries for complete species proteomes

  openvax/vaxrank#646 · Filter by author iskandr opened on Oct 16, 2026

• Expose optional WEIRDO foreignness evidence in epitope ranking and reports

  openvax/vaxrank#638 · Filter by author iskandr opened on Oct 15, 2026

• Use ORFdata host proteomes and species-scoped CTA evidence in shared manifests

  openvax/vaxrank#625 · Filter by author iskandr opened on Oct 14, 2026

• Adopt Topiary contextual caches for external candidate inference

  openvax/vaxrank#624 · Filter by author iskandr opened on Oct 13, 2026

• Unify CTA evidence admission for human, dog and mouse expression inputs

  openvax/vaxrank#596 · Filter by author iskandr opened on Oct 8, 2026
  2

• Adopt the mhctools documentation style

  openvax/vaxrank#561 · Filter by author iskandr opened on Oct 2, 2026

• examples/osteosarc_read_corpus: still wanted? plus resume invalidated by version/path churn and a 13-version-stale README

  openvax/vaxrank#532 · Filter by author iskandr opened on Sep 27, 2026

• Plan: rank DNA-only variants using optional expression evidence (patient bulk, or tissue/cancer-type proxy from oncoref)

  openvax/vaxrank#529 · Filter by author iskandr opened on Sep 27, 2026
  2

• Build Sid read cohorts as subsets of the shared OpenVax union panel (iskandr/osteosarc#56)

  openvax/vaxrank#522 · Filter by author iskandr opened on Sep 26, 2026
  1

• Remove hasattr/signature tests that stand in for the behavior they describe

  openvax/vaxrank#495 · Filter by author iskandr opened on Sep 21, 2026

• Report tests assert len(contents.split()) > 0, which is always true; plus duplicated and echo-only config tests

  openvax/vaxrank#494 · Filter by author iskandr opened on Sep 21, 2026
  1

• Use repository-relative source paths in visualization manifests

  openvax/vaxrank#472 · Filter by author iskandr opened on Sep 16, 2026

• Output path handling is spread across ten writers; bad paths fail only after the full run

  openvax/vaxrank#465 · Filter by author iskandr opened on Sep 16, 2026

• Two different rules decide which args are internal; the report and the run summary can disagree

  openvax/vaxrank#464 · Filter by author iskandr opened on Sep 16, 2026

• Help and summary accuracy: isovar defaults print as None, undocumented --log-path default, incomplete --print-default-config

  openvax/vaxrank#462 · Filter by author iskandr opened on Sep 15, 2026

• weasyprint PDF backend clips report tables off the right edge (loses the WT IC50 column)

  openvax/vaxrank#461 · Filter by author iskandr opened on Sep 15, 2026

• Console logging: everything on stdout, tqdm bar in non-TTY runs, object reprs at INFO, VCF parsed twice

  openvax/vaxrank#460 · Filter by author iskandr opened on Sep 15, 2026

• XLSX/CSV number hygiene: scores written as text, unnamed index column, full-precision VAF, chr/pos vs contig/start

  openvax/vaxrank#459 · Filter by author iskandr opened on Sep 15, 2026

• ASCII report: vaccine-construction rows run together, scores print as 0.000, manufacturability as 17-digit floats

  openvax/vaxrank#458 · Filter by author iskandr opened on Sep 15, 2026