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Claude Skills by antigenomics
github.com/antigenomics6 skills0 installs13 views
- Vdjdb DuplicatesAudit repeated TCR records across the whole VDJdb corpus - which clonotypes and pMHC pairs recur, whether a recurrence is a same-lab follow-up publication or independent replication (by PubMed author overlap), which within-chunk multiplicities are sequencing read depth rather than distinct clones, and which epitopes are recorded against inconsistent or genuinely multiple MHC restrictions. Use for a corpus-wide consistency audit or before landing a large chunk that may already be in the database.Votes: 0GitHub stars: 157
- Vdjdb ExtractExtract 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 source. Use when a paper, dataset or submitter folder has to become a chunk file, before vdjdb-format and vdjdb-proofread.Votes: 0GitHub stars: 157
- Vdjdb FormatNormalise 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 naming the authority behind every change. Use after vdjdb-extract and before vdjdb-proofread, or on any TSV whose gene or allele spellings need bringing to IMGT.Votes: 0GitHub stars: 157
- Vdjdb HarmonizeCanonicalise 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 that is a substring of another, and extend the alias tables where they have no entry. Use when antigen.gene or antigen.species carry free text rather than symbols, or when vdjdb-p...Votes: 0GitHub stars: 157
- Vdjdb ProofreadValidate 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 withheld/. Use as the last gate before a chunk is committed, or on any chunk suspected of having a column shift, bad gene or allele names, blank MHC fields or missing method informat...Votes: 0GitHub stars: 157
- Vdjdb PublishPublish 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.Votes: 0GitHub stars: 157