Skill Claude CodeCodex
Review repeated paired receptor-pMHC observations and metadata synonyms within and across VDJdb publications, preserving distinct experiments and reports. Use for a corpus audit or a submission that may overlap existing records.
Skill Claude CodeCodex
Extract TCR:pMHC specificity records from raw submission sources - supplementary XLS/CSV tables, PDF manuscripts, 10x Genomics contig and clonotype files, AIRR Rearrangement TSVs, Adaptive ImmunoSEQ exports - into a VDJdb chunk TSV, verifying every extracted sequence, gene, allele and reference id back against the…
Skill Claude CodeCodex
Normalise the controlled-vocabulary fields of a raw VDJdb chunk TSV to the form the database records - IMGT V/D/J gene and allele names including Adaptive ImmunoSEQ and Arden conversions, IPD-IMGT/HLA and murine H2 MHC allele names, species CamelCase, method vocabulary, reference id prefixes - and write a format log…
Skill Claude CodeCodex
Canonicalise antigen.gene and antigen.species in a VDJdb chunk against the epitope dictionary and the gene and species alias tables, detect spurious values (UniProt descriptions, "[species]" annotations, "Probable"/"Chain A," prefixes, multi-word organism names), resolve blanks from the publication, flag one epitope…
Skill Claude CodeCodex
Validate a VDJdb chunk with vdjdb qc and vdjdb submission, explain every finding with a specific suggested fix and the authority behind it, resolve method-field and MHC problems the rules cannot decide, read the junction-versus-germline and score reports, and decide whether the chunk lands in chunks/, pending/ or…
Skill Claude CodeCodex
Publish proofread VDJdb chunks through dev, reconcile publication issues, preserve record identity, keep validation changes separate, and close completed imports while tracking unresolved observations and optional metadata follow-ups. Use when a chunk is ready to publish or an imported paper needs closeout.
Skill Claude CodeCodex
Validate VDJdb build code, CI, output contracts and release promotions against a released corpus. Use for build changes, dependency upgrades, integration audits and release orchestration; route manual source extraction and curation decisions to the curation skills.
Skill Claude CodeCodex
Extract and proofread deposited TCR-pMHC observations with the local tcren pipeline, then update the PDB aggregate chunk. Use for a structural publication or missing PDB entries; exclude predicted docking models and complexes without supported receptor-pMHC assignments.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: