scientific-writinglisted

Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods, generate figure legends, create supplementary tables, draft data availability statements, compile tool citations, or auto-generate any publication text from their ENCODE analysis. Trigger on: methods section, figure legend, supplementary table, data availability, tool citations, publication writing, manuscript, write methods, methods draft, write up, write-up, paper writing, reproducible methods.
ammawla/encode-toolkit · ★ 35 · Data & Documents · score 79

Install: claude install-skill ammawla/encode-toolkit

# Scientific Writing from ENCODE Provenance Generate publication-quality scientific writing from ENCODE analysis records. This skill integrates with `data-provenance` and `cite-encode` to auto-generate methods from logged pipeline runs. Every generated section follows rigorous scientific documentation standards -- complete reporting of all experimental and computational parameters with zero ambiguity. ## When to Use - User wants to write publication-ready methods sections, figure legends, or data availability statements - User asks about "methods section", "figure legend", "scientific writing", or "manuscript preparation" - User needs to auto-generate methods text from logged provenance/analysis steps - User wants templates for supplementary tables, Key Resources Tables, or tool citation formatting - Example queries: "write a methods section for my ChIP-seq analysis", "generate a figure legend for my heatmap", "format my data availability statement" ## Overview Most methods sections in genomics papers are incomplete. They omit software versions, skip reference file details, conflate technical and biological replicates, and use phrases like "default parameters" without stating what those defaults are. Reviewers catch these omissions, and readers cannot reproduce the analysis. This skill solves the problem by generating methods text directly from the provenance chain. When every processing step has been logged (via `data-provenance`), the methods section writes itself. Wh