By antigenomics

Publish proofread VDJdb chunks through dev, reconcile publication issues, preserve record identity, keep validation changes separate, and close completed imports while tracking unresolved…

antigenomics/vdjdb-db

Validate VDJdb build code, CI, output contracts and release promotions against a released corpus.

antigenomics/vdjdb-db

Review repeated paired receptor-pMHC observations and metadata synonyms within and across VDJdb publications, preserving distinct experiments and reports.

antigenomics/vdjdb-db

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…

antigenomics/vdjdb-db

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]"…

antigenomics/vdjdb-db

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…

antigenomics/vdjdb-db

Extract and proofread deposited TCR-pMHC observations with the local tcren pipeline, then update the PDB aggregate chunk.

antigenomics/vdjdb-db

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…

antigenomics/vdjdb-db