v2.3.0

cerebroAppLite 2.3.0

HLA & TCR Motifs

• New page: HLA & TCR Motifs. A standalone top-level tab (peer of Immune
  Repertoire) that draws a CDR3 motif network — every unique CDR3 is a node and
  an edge joins two equal-length CDR3s at Hamming distance 1 — alongside
  donor-level HLA context. It appears conditionally, only when the loaded .crb
  carries a TRA/TRB chain. Three sub-tabs: Motif Network (colour by motif
  cluster, cell type, MHC context, HLA carrier status, or sample of origin),
  HLA Associations (descriptive carrier vs. non-carrier overlap — no p-value,
  no restriction claim), and Data & QC (coverage, normalized typing, and a
  session-only HLA upload).
• HLA typing on the data class. Cerebro_v1.3 gained an optional
  hla_typing slot with addHLATyping() / getHLATyping(); the getter is
  backward-compatible with older .crb files. Typing accepts a canonical long
  table, a wide sample + HLA-*_1/_2 table, or a named list, and carries
  provenance (genotyped / imputed / synthetic / unknown) so a synthetic
  or imputed genotype is never treated as directly typed.
• Export picks it up automatically. exportFromSeurat() now reads
  object@misc$hla_typing (with object@misc$hla_typing_source_type), parallel
  to the existing immune_repertoire slot.
• Declared contracts for bulk data. A .crb may declare
  observation_unit, receptor_key, and tcr_selection in technical_info, so
  the page states honestly when rows are analysis units rather than cells, when a
  receptor is keyed by V gene + CDR3, and when a carrier contrast is a positive
  control rather than independent evidence.
• One demo data set. demo_hla_tcr_dextramer.crb: 12,000 real CD8+ T cells,
  every one with a paired αβ clonotype, plus the donors' published HLA
  genotypes, from 10x Genomics' dextramer cohort (Zhang et al., Sci Adv 2021,
  CC-BY). The repertoire is antigen-selected, which is what makes its motif
  network legible on measured sequences, where an unselected repertoire gives a
  handful of disconnected dots. Class I only (sorted CD8+), so the Class I ×
  Class II pair scope stays hidden on this demo and appears when a data set
  carries Class II typing plus a lineage column.
  The per-cell dextramer_* columns are 10x's raw binder calls for a
  reagent, not validated peptide specificity: staining is heavily
  cross-reactive here, and a restriction_in_genotype (yes / no /
  unknown) column ships beside them so that is visible in the app rather than
  only in the vignette. unknown is not padding: table S1 publishes one HLA-B
  allele for two donors, and absence from an incompletely called locus is not
  evidence of absence. The HLA association contrasts use the published genotypes
  and are therefore not circular — though the repertoire was still captured by a
  reagent panel, so ascertainment and donor/panel confounding remain, which the
  caveat above the tables now states.
• Three new vignettes. "HLA & TCR Motifs: from synthetic data to an
  interactive app" (single-cell, runnable end to end), "HLA Associations on
  bulk TCRβ with real donor HLA" (bring your own bulk cohort, with its
  positive-control caveat), and "Antigen-selected single-cell TCR" (the
  shipped demo's full download → .crb pipeline).

What's Changed

• feat(hla): HLA & TCR Motifs page (2.3.0) by @duocang in #88

Full Changelog: v2.2.0...v2.3.0