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ChenHsieh/agentic-research-toolkit

Portable agentic research workflows (SKILL.md) written for discovery over confirmation

↗ GitHub ★ 0 NOASSERTION updated today project Claude Code
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ARCHETYPE
Skill Collector
Ten-plus skills loaded on demand. A procedural-knowledge library.
CONTEXT TAX · EVERY TURN
~2.1k tokens
Moderate · median rig: 2.3k · breakdown
GUARDRAILS
0/5
No committed guardrails · details

Copy this rig

# review before running: this installs third-party code
$ npx degit ChenHsieh/agentic-research-toolkit/skills ./rig-agentic-research-toolkit/skills

MCP servers are added to Claude Code at local scope; env vars are shown as YOUR_… placeholders — we never store values. Files are fetched with degit into a separate folder so you can review before merging.

$ npx degit ChenHsieh/agentic-research-toolkit/skills/accession-paper-crosswalk .claude/skills/accession-paper-crosswalk
$ npx degit ChenHsieh/agentic-research-toolkit/skills/design-confound-audit .claude/skills/design-confound-audit
$ npx degit ChenHsieh/agentic-research-toolkit/skills/ecosystem-mapper .claude/skills/ecosystem-mapper
$ npx degit ChenHsieh/agentic-research-toolkit/skills/ml-genomics-best-practices .claude/skills/ml-genomics-best-practices
$ npx degit ChenHsieh/agentic-research-toolkit/skills/result-autopsy .claude/skills/result-autopsy
$ npx degit ChenHsieh/agentic-research-toolkit/skills/scientific-schematics .claude/skills/scientific-schematics
$ npx degit ChenHsieh/agentic-research-toolkit/skills/second-opinion-concordance .claude/skills/second-opinion-concordance
$ npx degit ChenHsieh/agentic-research-toolkit/skills/statistic-null .claude/skills/statistic-null
$ npx degit ChenHsieh/agentic-research-toolkit/skills/tikz-figures .claude/skills/tikz-figures
$ npx degit ChenHsieh/agentic-research-toolkit/skills/trait-gene-miner .claude/skills/trait-gene-miner

This rig commits no guardrails. Here is the community baseline instead — the deny/ask rules most often found across all 7,204 rigs:

{
  "permissions": {
    "deny": [
      "Read(./.env)",
      "Read(**/.env)",
      "Read(~/.ssh/**)",
      "Bash(rm -rf *)",
      "Read(**/*.pem)",
      "Bash(rm -rf /)",
      "Bash(git push --force:*)",
      "Bash(sudo *)",
      "Read(.env)",
      "Bash(rm -rf /*)",
      "Read(./.env.*)",
      "Read(~/.aws/**)",
      "Bash(git push --force*)",
      "Bash(rm -rf:*)",
      "Read(**/*.key)",
      "Read(**/.env.*)",
      "Bash(sudo:*)",
      "Bash(git reset --hard*)",
      "Bash(git reset --hard:*)",
      "Read(.env.*)"
    ],
    "ask": [
      "Bash(git push:*)",
      "Bash(git push *)",
      "Bash(git commit:*)",
      "Bash(rm *)",
      "Bash(rm:*)",
      "Bash(git rebase *)",
      "Bash(wget *)",
      "Bash(npm publish:*)",
      "Bash(git commit *)",
      "Bash(gh pr merge *)"
    ]
  }
}

Skills (10)

accession-paper-crosswalkdesign-confound-auditecosystem-mapperml-genomics-best-practicesresult-autopsyscientific-schematicssecond-opinion-concordancestatistic-nulltikz-figurestrait-gene-miner

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