---
name: geo-biomarker-html-report
description: Use when the user wants a GEO/GSE dataset turned into a real reproducible report bundle, says 生成HTML报告 / 直接运行 / 复现这个报告 / 同步生成中文HTML / 导出分析代码和结果图, wants a Nature-like research-first supplement style, or asks to package the end-to-end go-to-report workflow into a reusable skill.
---

# GEO Biomarker HTML Report

## Overview

Turn a user’s “go” request into a real, rerunnable GEO-based report **delivery bundle** with HTML, figures, manifest files, exported analysis code, and a final bundle path. Default to a light academic / Nature-supplement feel unless the user explicitly asks for a darker dashboard style. When the user asks for Chinese同步版, the default deliverable becomes paired outputs: `report.html` and `report_zh.html`.

Open `references/workflow.md` when you need the detailed execution checklist, output contract, command examples, or common pitfalls.

## Use This Skill To

- reproduce the structure or feel of an existing biomarker report with a new GSE dataset;
- build or adapt a local report pipeline that ends in a bundled run directory, not just a single HTML file;
- emit synchronized English + Chinese HTML companions from one verified analysis run;
- export the runnable analysis code, result figures, PDF figure copies, tables, and manifest into the same delivery folder;
- keep analysis claims strictly aligned to the dataset’s true data types;
- package the successful workflow itself into a reusable personal skill.

## Do Not Use This Skill When

- the user only wants a manuscript, abstract, or slide deck;
- the request is just for generic dashboard UI without a scientific analysis pipeline;
- the dataset is not GEO/GSE-like and the main problem is elsewhere.

## Workflow Summary

1. Start from the raw need, not the surface phrasing. Lock what is being reproduced: **style**, **analysis scope**, or both.
2. Inspect local inputs first: project files, report templates, webarchives, PDFs, configs, and prior outputs.
3. Declare the reproducibility boundary before analysis. Processed expression is not raw counts.
4. Reuse an existing local pipeline when it already matches the need; otherwise scaffold the smallest reproducible project.
5. Keep the report modular and skill-labeled, but keep the execution path simple and local.
6. Export a delivery bundle in the same run directory: HTML, markdown/context, tables/data, PNG figures, PDF figures, and `analysis_code/`.
7. If the user wants bilingual delivery, keep figures/tables/manifest shared and localize only the reading layer.
8. Use tests before behavior changes, then run the full end-to-end command before claiming success.
9. If the user asks to package the workflow, create the skill in `~/.claude/skills/` and symlink it into `~/.codex/skills/`.

## Style Defaults

- light, research-first, publication-adjacent;
- subtle accent color, not product-dashboard contrast;
- long sidebar labels must wrap cleanly;
- provenance metadata should sit in a quiet footer/meta block;
- if the report is long, prefer a subtle active-section sidebar highlight.
- if Chinese HTML is requested, translate section titles, narrative copy, and footer metadata while keeping skill badges stable for provenance.
- bundle contents should be organized so an external collaborator can open one run directory and find code, figures, tables, and HTML without hunting across the project.

## Delivery Rules

- Surface exact output paths.
- Default deliverable = the whole run directory, not only `report.html`.
- If bilingual mode is enabled, surface both HTML paths explicitly.
- Also surface `analysis_code/`, `figures/`, `figures/pdf/`, `tables/`, and `data/` paths.
- Separate direct dataset results from external evidence enrichment.
- Report the analysis branch explicitly in the final summary.
- Do fresh verification immediately before any completion claim.
