vdjdb-extract
Extract TCR:pMHC specificity data from raw source files (papers, supplementary tables, XLS, PDF, 10X output, AIRR-format) and produce a VDJdb-formatted TSV chunk ready for /format and /proofread.
Browse reusable Agent Skills, each with a clear purpose and practical guidance.
Extract TCR:pMHC specificity data from raw source files (papers, supplementary tables, XLS, PDF, 10X output, AIRR-format) and produce a VDJdb-formatted TSV chunk ready for /format and /proofread.
Standardise a raw or partially-formatted VDJdb TSV chunk — normalising species names, IMGT V/D/J gene IDs, IMGT-HLA MHC alleles, and method vocabulary — and produce a properly-named chunk file ready for proofreading.
Harmonize antigen.gene and antigen.species fields in a VDJdb chunk to canonical VDJdb naming. Detects spurious gene/species names, resolves inconsistencies (same epitope → multiple names), and warns about epitopes that are exact substrings of longer epitopes. Invoked standalone or from /proofread when spurious values are detected.
Translate visa application documents (images) to English and create a bilingual PDF with original and translation
Reviews a non-disclosure agreement against the firm's NDA checklist and reports findings with citations. Use when the user attaches an NDA and asks to check or review it.
Distill a research directory (produced by /research) into a single compact research.md containing a guideline-relative distillation of only the sources that were actually used in a piece of content. Use this skill whenever the user wants to extract used references from research, create a research appendix for an article, distill research into what was actually cited, or produce a portable reference file from a research directory. Trigger when the user says things like "distill my research", "extract used sources", "which research did I actually use", "create research.md", "compile references from research", or after finishing an article that used a research directory.
Generate a multi-form answer (Marp slide deck, matplotlib chart, Obsidian Canvas, or social content brief) from one or more wiki pages in a research directory and file the output back into wiki/renders/. Outputs compound — they appear in index.yaml/index.md and can be re-rendered idempotently. One run can render several forms at once. Use when the user wants to "make a slide deck on X", "chart the comparison of A vs B", "build a canvas of how these concepts connect", "render this as Marp", or "extract a post idea / content brief from my research". Trigger on phrasings like "render", "slide deck", "chart", "canvas", "marp", "brief", "post idea", "extract ideas for social".
System clipboard — copy, paste, transform content between clipboard and files.