Maps TCR/BCR receptor sequences toward candidate antigen specificity and clusters repertoires by shared-specificity signal, while enforcing that a database match or a cluster label is a HYPOTHESIS, not a specificity call. Use when deciding among database annotation (VDJdb/McPAS/IEDB+TCRMatch, requiring V-gene and HLA concordance plus a confidence score) versus sequence clustering (tcrdist3 meta-clonotypes, GLIPH2, GIANA, clusTCR, which find enrichment not per-receptor labels) versus generation-probability nulls (OLGA Pgen, IGoR, SONIA Ppost) for testing public/convergent/shared claims; and when guarding against overclaiming specificity, base-rate false positives from bare CDR3 matches, unpaired beta-only annotation, ML predictor failure on unseen epitopes, and ignored MHC restriction. TCR-focused with a BCR/antibody note (SHM, conformational epitopes, IGHV3-53/3-66 public clonotypes). Keywords CDR3, pMHC, HLA restriction, cross-reactivity, meta-clonotype, Pgen, public clonotype, convergent recombination.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryScience & researchStars0
About this skill
Maps TCR/BCR receptor sequences toward candidate antigen specificity and clusters repertoires by shared-specificity signal, while enforcing that a database match or a cluster label is a HYPOTHESIS, not a specificity call. Use when deciding among database annotation (VDJdb/McPAS/IEDB+TCRMatch, requiring V-gene and HLA concordance plus a confidence score) versus sequence clustering (tcrdist3 meta-clonotypes, GLIPH2, GIANA, clusTCR, which find enrichment not per-receptor labels) versus generation-probability nulls (OLGA Pgen, IGoR, SONIA Ppost) for testing public/convergent/shared claims; and when guarding against overclaiming specificity, base-rate false positives from bare CDR3 matches, unpaired beta-only annotation, ML predictor failure on unseen epitopes, and ignored MHC restriction. TCR-focused with a BCR/antibody note (SHM, conformational epitopes, IGHV3-53/3-66 public clonotypes). Keywords CDR3, pMHC, HLA restriction, cross-reactivity, meta-clonotype, Pgen, public clonotype, convergent recombination.
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Maps TCR/BCR receptor sequences toward candidate antigen specificity and clusters repertoires by shared-specificity signal, while enforcing that a database match or a cluster label is a HYPOTHESIS, not a specificity call. Use when deciding among database annotation (VDJdb/McPAS/IEDB+TCRMatch, requiring V-gene and HLA concordance plus a confidence score) versus sequence clustering (tcrdist3 meta-clonotypes, GLIPH2, GIANA, clusTCR, which find enrichment not per-receptor labels) versus generation-probability nulls (OLGA Pgen, IGoR, SONIA Ppost) for testing public/convergent/shared claims; and when guarding against overclaiming specificity, base-rate false positives from bare CDR3 matches, unpaired beta-only annotation, ML predictor failure on unseen epitopes, and ignored MHC restriction. TCR-focused with a BCR/antibody note (SHM, conformational epitopes, IGHV3-53/3-66 public clonotypes). Keywords CDR3, pMHC, HLA restriction, cross-reactivity, meta-clonotype, Pgen, public clonotype, convergent recombination.
About this listing
Category
Science & research
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI