/deep-research

by Edward Cheng-I Wuimbad0202/academic-research-skills50k stars

3,864

Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 8 modes: full research, quick brief, paper review, lit-review, fact-check, three-way literature scan, Socratic guided research dialogue, and systematic review with optional meta-analysis. Covers research question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk of bias assessment, meta-analysis, APA 7.0 report compilation, editorial review, devil's advocate challenges, ethics review, and post-research literature monitoring. Triggers on: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, WHY HOW WHAT papers, 3W literature scan, guide my research, help me think through, 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 三段式文獻掃描, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題, 심층 연구, 문헌 조사, 체계적 문헌고찰, 메타분석, 사실 확인, 연구 방향을 잡아줘, 연구 주제 정하는 것을 도와줘, revisión de literatura, metaanálisis

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templatesliterature_matrix_template.md

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Literature Matrix Template

Purpose

Source x Theme cross-tabulation for systematic evidence mapping. Used by the synthesis_agent to organize evidence before writing the synthesis narrative.

Matrix Structure

Basic Matrix

## Literature Matrix: [Research Topic]

**Date compiled**: [YYYY-MM-DD]
**Total sources**: [N]
**Themes identified**: [N]

| Source | Year | Level | Theme A | Theme B | Theme C | Theme D | Theme E |
|--------|------|-------|---------|---------|---------|---------|---------|
| Author1 | 2024 | II | ✓ Supports | — | ✓ Supports | ✗ Contradicts | — |
| Author2 | 2023 | III | ✓ Supports | ✓ Supports | — | — | ✓ Supports |
| Author3 | 2022 | VI | — | ✓ Supports | ✓ Supports | ✓ Supports | — |
| Author4 | 2024 | I | ✓ Supports | ✓ Supports | ✗ Contradicts | — | ✓ Supports |
| Author5 | 2023 | IV | ✗ Contradicts | — | ✓ Supports | ✓ Supports | — |
| **Totals** | | | **4✓ 1✗** | **3✓ 0✗** | **3✓ 1✗** | **2✓ 1✗** | **2✓ 0✗** |

### Legend
- ✓ Supports: Source provides evidence supporting this theme
- ✗ Contradicts: Source provides evidence contradicting this theme
- — : Source does not address this theme
- Level: Evidence hierarchy level (I = highest, VII = lowest)

Extended Matrix (with detail)

## Extended Literature Matrix

| Source | Method | Sample | Theme A: [name] | Theme B: [name] | Quality |
|--------|--------|--------|-----------------|-----------------|---------|
| Author1 (2024) | RCT, N=500 | University students, US | "Finding X was significant (p<.001)" — Supports | Not addressed | A |
| Author2 (2023) | Case study, N=3 institutions | Asian universities | "Institution A showed..." — Supports | "However, in context B..." — Partial | C |
| Author3 (2022) | Meta-analysis, k=42 | Global | "Pooled effect size d=0.45" — Strong support | "Subgroup analysis revealed..." — Mixed | A |

Convergence Summary

## Evidence Convergence Summary

| Theme | Sources For | Sources Against | Net | Strength | Confidence |
|-------|-----------|----------------|-----|----------|-----------|
| Theme A | 4 (Levels I, II, III, IV) | 1 (Level VI) | +3 | Strong | High |
| Theme B | 3 (Levels I, III, IV) | 0 | +3 | Strong | High |
| Theme C | 3 (Levels II, III, VI) | 1 (Level I) | +2 | Contested | Medium |
| Theme D | 2 (Levels IV, VI) | 1 (Level II) | +1 | Weak | Low |
| Theme E | 2 (Levels I, III) | 0 | +2 | Moderate | Medium |

### Interpretation Guide
- **Strong** (≥3 supporting, higher-level evidence): Confident finding
- **Moderate** (2-3 supporting, mid-level evidence): Likely finding, more evidence welcome
- **Weak** (1-2 supporting, lower-level evidence): Tentative, needs more research
- **Contested** (evidence on both sides): Genuine debate, report both sides
- **Gap** (0 sources): Knowledge gap identified

Gap Identification

## Knowledge Gaps

| Gap | Type | Implication | Priority |
|-----|------|-------------|----------|
| No data on [population X] | Empirical | Cannot generalize to this group | High |
| Only [method type] used | Methodological | Triangulation needed | Medium |
| No studies since [year] | Temporal | Evidence may be outdated | Medium |
| Only studied in [region] | Geographic | Generalizability unknown | Low |
| No theoretical framework for [finding] | Theoretical | Theory development opportunity | Low |

Usage Notes

Start with the Basic Matrix for initial organization
Upgrade to Extended Matrix as synthesis deepens
Convergence Summary should directly inform the synthesis narrative
Gap Identification feeds into the Discussion section
Update the matrix as new sources are added — it is a living document

Source: SKILL.md on GitHub

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The deep-research skill is a highly sophisticated research orchestration system that includes robust internal security instructions to prevent prompt injection from untrusted data. It leverages well-known scholarly APIs for data verification and uses local scripts for deterministic validation of research artifacts.
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Signed by skilld at c5c1b45. This ties the file your Agent reads to that commit on GitHub. It does not review the instructions.

Last checked against GitHub 33 minutes ago.

Activeupdated 2 days ago

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Other metadata

metadata: { "version": "2.12.1", "last_updated": "2026-08-15", "status": "active", "data_access_level": "raw", "task_type": "open-ended", "related_skills": [ "academic-paper", "academic-pipeline" ] }