@wentorai/research-plugins 1.0.0 → 1.1.0

package/README.md

@@ -8,7 +8,7 @@
 
 ## Research Plugins for Research-Claw
 
-An open-source collection of **173 academic research skills**, **61 MCP server configs**, **13 agent tools**, and **6 curated resource lists** for [Research-Claw](https://wentor.ai) and other AI coding agents.
+An open-source collection of **349 academic research skills**, **76 MCP configs**, **13 agent tools**, and **6 curated resource lists** for [Research-Claw](https://wentor.ai) and other AI coding agents.
 
 Built by [Wentor AI](https://wentor.ai) for the global research community.
 
@@ -16,23 +16,23 @@ Built by [Wentor AI](https://wentor.ai) for the global research community.
 
 | Component | Count | Description |
 |-----------|-------|-------------|
-| **Skills** | 173 | Practical SKILL.md guides covering literature search, academic writing, data analysis, research methods, 16 domain specialties, and productivity tools |
+| **Skills** | 349 | Practical SKILL.md guides covering literature search, academic writing, data analysis, research methods, 16 domain specialties, and productivity tools |
 | **Agent Tools** | 13 | TypeScript API wrappers for Semantic Scholar, OpenAlex, CrossRef, arXiv, PubMed, and Unpaywall |
-| **MCP Configs** | 61 | Ready-to-use MCP server configurations for reference managers, knowledge bases, research databases, and AI platforms |
+| **MCP Configs** | 76 | Ready-to-use MCP server configurations for reference managers, knowledge bases, research databases, and AI platforms |
 | **Curated Lists** | 6 | Hand-picked resource collections for each skill category |
 
 ### Taxonomy
 
 Skills are organized into **6 categories** with **40 subcategories**:
 
-| Category | Subcategories | Skills |
-|----------|---------------|--------|
-| **literature** | search, discovery, fulltext, metadata | Paper search, citation tracking, open access |
-| **writing** | composition, polish, latex, templates, citation | Academic writing, LaTeX, reference management |
-| **analysis** | statistics, econometrics, wrangling, dataviz | Statistical methods, data cleaning, visualization |
-| **research** | methodology, deep-research, paper-review, automation, funding | Research design, systematic reviews, grant writing |
-| **domains** | 16 disciplines (CS, AI/ML, biomedical, chemistry, economics, finance, law, physics, math, ecology, etc.) | Domain-specific research methods and tools |
-| **tools** | diagram, document, code-exec, scraping, knowledge-graph, ocr-translate | Diagrams, PDF parsing, reproducible code, OCR |
+| Category | Subcategories | Skills | Description |
+|----------|---------------|--------|-------------|
+| **literature** | search, discovery, fulltext, metadata | 50 | Paper search, citation tracking, open access |
+| **writing** | composition, polish, latex, templates, citation | 57 | Academic writing, LaTeX, reference management |
+| **analysis** | statistics, econometrics, wrangling, dataviz | 47 | Statistical methods, data cleaning, visualization |
+| **research** | methodology, deep-research, paper-review, automation, funding | 56 | Research design, systematic reviews, grant writing |
+| **domains** | 16 disciplines (CS, AI/ML, biomedical, chemistry, economics, finance, law, physics, math, ecology, etc.) | 97 | Domain-specific research methods and tools |
+| **tools** | diagram, document, code-exec, scraping, knowledge-graph, ocr-translate | 42 | Diagrams, PDF parsing, reproducible code, OCR |
 
 ### Install
 
@@ -115,7 +115,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines on adding skills, MCP conf
 
 ## Research-Claw 科研插件集
 
-一个开源的学术科研资源集合，包含 **173 个科研技能**、**61 个 MCP 服务器配置**、**13 个智能体工具** 和 **6 个精选资源列表**，为 [Research-Claw (科研龙虾)](https://wentor.ai) 及其他 AI 编程助手而构建。
+一个开源的学术科研资源集合，包含 **349 个科研技能**、**76 个 MCP 服务器配置**、**13 个智能体工具** 和 **6 个精选资源列表**，为 [Research-Claw (科研龙虾)](https://wentor.ai) 及其他 AI 编程助手而构建。
 
 由 [Wentor AI](https://wentor.ai) 为全球科研社区打造。
 
@@ -123,23 +123,23 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines on adding skills, MCP conf
 
 | 组件 | 数量 | 说明 |
 |------|------|------|
-| **技能 (Skills)** | 173 | 涵盖文献检索、学术写作、数据分析、研究方法、16 个学科领域及生产力工具的实用指南 |
+| **技能 (Skills)** | 349 | 涵盖文献检索、学术写作、数据分析、研究方法、16 个学科领域及生产力工具的实用指南 |
 | **智能体工具** | 13 | 封装 Semantic Scholar、OpenAlex、CrossRef、arXiv、PubMed、Unpaywall 六大学术 API 的 TypeScript 工具 |
-| **MCP 配置** | 61 | 即用型 MCP 服务器配置，涵盖文献管理、知识库、学术数据库、AI 平台等 |
+| **MCP 配置** | 76 | 即用型 MCP 服务器配置，涵盖文献管理、知识库、学术数据库、AI 平台等 |
 | **精选列表** | 6 | 按分类整理的优质资源推荐 |
 
 ### 分类体系
 
 技能按 **6 大类别** 和 **40 个子分类** 组织：
 
-| 类别 | 子分类 | 覆盖范围 |
-|------|--------|---------|
-| **文献 (literature)** | 检索、发现、全文获取、元数据 | 论文搜索、引文追踪、开放获取 |
-| **写作 (writing)** | 写作、润色、LaTeX、模板、引用 | 学术写作、LaTeX 排版、参考文献管理 |
-| **分析 (analysis)** | 统计、计量经济、数据处理、可视化 | 统计方法、数据清洗、图表制作 |
-| **研究 (research)** | 方法论、深度研究、论文评审、自动化、基金 | 研究设计、系统综述、基金申请 |
-| **学科 (domains)** | 16 个学科方向 | 各学科专属研究方法与工具 |
-| **工具 (tools)** | 图表、文档、代码执行、爬虫、知识图谱、OCR | 流程图、PDF 解析、可复现代码、OCR 翻译 |
+| 类别 | 子分类 | 技能数 | 覆盖范围 |
+|------|--------|--------|---------|
+| **文献 (literature)** | 检索、发现、全文获取、元数据 | 50 | 论文搜索、引文追踪、开放获取 |
+| **写作 (writing)** | 写作、润色、LaTeX、模板、引用 | 57 | 学术写作、LaTeX 排版、参考文献管理 |
+| **分析 (analysis)** | 统计、计量经济、数据处理、可视化 | 47 | 统计方法、数据清洗、图表制作 |
+| **研究 (research)** | 方法论、深度研究、论文评审、自动化、基金 | 56 | 研究设计、系统综述、基金申请 |
+| **学科 (domains)** | 16 个学科方向 | 97 | 各学科专属研究方法与工具 |
+| **工具 (tools)** | 图表、文档、代码执行、爬虫、知识图谱、OCR | 42 | 流程图、PDF 解析、可复现代码、OCR 翻译 |
 
 ### 安装方式
 

package/curated/analysis/README.md

@@ -1,64 +1,79 @@
-# Curated Analysis Resources
+# Analysis — Curated Skills
 
-> Hand-picked resources for academic researchers working with statistics, econometrics, data wrangling, and visualization.
 
-## Statistics
+> 47 recommended skills for data analysis, statistics, visualization, and econometrics.
+
 
-### Tools & Software (R)
-- **[tidyverse](https://www.tidyverse.org/)** — Opinionated collection of R packages (dplyr, ggplot2, tidyr, etc.) for tidy data analysis.
-- **[R for Data Science (2e)](https://r4ds.hadley.nz/)** — Free online book by Hadley Wickham; the definitive introduction to data science in R.
-- **[statsmodels](https://www.statsmodels.org/)** — Python module for statistical modeling, hypothesis tests, and regression diagnostics.
-- **[JASP](https://jasp-stats.org/)** — Free, open-source GUI for Bayesian and frequentist statistics; great for teaching and exploratory analysis.
+## Dataviz
 
-### Tools & Software (Python)
-- **[SciPy](https://scipy.org/)** — Fundamental library for scientific computing; stats, optimization, linear algebra.
-- **[pingouin](https://pingouin-stats.org/)** — Simple, pandas-friendly Python package for common statistical tests (ANOVA, t-tests, correlations).
-- **[PyMC](https://www.pymc.io/)** — Probabilistic programming library for Bayesian statistical modeling and inference.
 
-### Key References
-- **[An Introduction to Statistical Learning (ISLR)](https://www.statlearning.com/)** — Free textbook with R and Python labs; accessible introduction to modern statistics and machine learning.
-- **[Seeing Theory](https://seeing-theory.brown.edu/)** — Interactive visual introduction to probability and statistics from Brown University.
-- **[Common statistical tests are linear models](https://lindeloev.github.io/tests-as-linear/)** — Concise reference showing that t-tests, ANOVA, chi-squared, etc. are all special cases of the linear model.
+| Skill | Description |
+|-------|-------------|
+| [algorithm-visualizer-guide](../../skills/analysis/dataviz/algorithm-visualizer-guide/) | Guide to Algorithm Visualizer for interactive algorithm exploration |
+| [bokeh-visualization-guide](../../skills/analysis/dataviz/bokeh-visualization-guide/) | Guide to Bokeh for interactive browser-based research visualizations |
+| [chart-image-generator](../../skills/analysis/dataviz/chart-image-generator/) | Generate publication-quality chart images from research data |
+| [color-accessibility-guide](../../skills/analysis/dataviz/color-accessibility-guide/) | Colorblind-friendly palettes and accessible visualization design |
+| [d3-visualization-guide](../../skills/analysis/dataviz/d3-visualization-guide/) | Guide to D3.js for building custom interactive data visualizations |
+| [echarts-visualization-guide](../../skills/analysis/dataviz/echarts-visualization-guide/) | Guide to Apache ECharts for interactive research data dashboards |
+| [geospatial-viz-guide](../../skills/analysis/dataviz/geospatial-viz-guide/) | Create maps, choropleths, and spatial data visualizations for research |
+| [interactive-viz-guide](../../skills/analysis/dataviz/interactive-viz-guide/) | Interactive data visualization with Plotly, ECharts, and D3 |
+| [metabase-analytics-guide](../../skills/analysis/dataviz/metabase-analytics-guide/) | Guide to Metabase for open-source research data analytics and dashboards |
+| [network-visualization-guide](../../skills/analysis/dataviz/network-visualization-guide/) | Visualize networks, graphs, citation maps, and relational data |
+| [plotly-interactive-guide](../../skills/analysis/dataviz/plotly-interactive-guide/) | Guide to Plotly.py for interactive scientific visualizations in Python |
+| [publication-figures-guide](../../skills/analysis/dataviz/publication-figures-guide/) | Create journal-quality scientific figures with proper styling and accessibility |
+| [python-dataviz-guide](../../skills/analysis/dataviz/python-dataviz-guide/) | Publication-quality data visualization with matplotlib, seaborn, and plotly |
+| [redash-analytics-guide](../../skills/analysis/dataviz/redash-analytics-guide/) | Guide to Redash for SQL-driven research data dashboards and sharing |
+
 
 ## Econometrics
 
-### Tools & Software
-- **[Stata](https://www.stata.com/)** — Industry-standard software for econometric analysis; excellent documentation and community (ado files).
-- **[linearmodels (Python)](https://bashtage.github.io/linearmodels/)** — Panel data, IV, and system regression models for Python; extends statsmodels.
-- **[fixest (R)](https://lrberge.github.io/fixest/)** — Blazing-fast fixed-effects estimation in R; supports multi-way clustering and IV.
-- **[CausalInference (Python)](https://causalinferenceinpython.org/)** — Open tutorials on difference-in-differences, RDD, IV, and synthetic control in Python.
-
-### Key References
-- **[Causal Inference: The Mixtape (Cunningham)](https://mixtape.scunning.com/)** — Free online textbook covering modern causal inference methods with Stata and R code.
-- **[The Effect (Huntington-Klein)](https://theeffectbook.net/)** — Free book on research design and causal inference; R and Python examples.
-- **[Mostly Harmless Econometrics](https://www.mostlyharmlesseconometrics.com/)** — Angrist and Pischke's concise guide to applied econometric methods.
-
-## Data Wrangling
-
-### Tools & Software
-- **[pandas](https://pandas.pydata.org/)** — The core Python library for tabular data manipulation and analysis.
-- **[Polars](https://pola.rs/)** — Lightning-fast DataFrame library in Rust with Python bindings; ideal for large datasets.
-- **[OpenRefine](https://openrefine.org/)** — Free tool for cleaning messy data, reconciling entities, and transforming formats.
-- **[data.table (R)](https://rdatatable.gitlab.io/data.table/)** — High-performance R package for fast aggregation and joins on large data.
-
-### Online Courses & Tutorials
-- **[Pandas Getting Started Tutorials](https://pandas.pydata.org/docs/getting_started/intro_tutorials/)** — Official step-by-step tutorials covering core pandas operations.
-- **[Tidy Data (Wickham, 2014)](https://www.jstatsoft.org/article/view/v059i10)** — Foundational paper on data structure principles; essential reading before any analysis.
-
-## Data Visualization
-
-### Plotting Libraries
-- **[Matplotlib](https://matplotlib.org/)** — Foundational Python plotting library; full control over every element.
-- **[ggplot2](https://ggplot2.tidyverse.org/)** — Grammar of Graphics implementation in R; the gold standard for statistical graphics.
-- **[Plotly](https://plotly.com/python/)** — Interactive, publication-quality charts in Python, R, and JavaScript.
-- **[Observable Plot](https://observablehq.com/plot/)** — Concise JavaScript plotting library for exploratory data visualization.
-- **[seaborn](https://seaborn.pydata.org/)** — High-level Python interface to Matplotlib for attractive statistical graphics.
-
-### Color Palettes & Design
-- **[ColorBrewer](https://colorbrewer2.org/)** — Cartographer-designed color schemes that are colorblind-safe and print-friendly.
-- **[Scientific Colour Maps (Crameri)](https://www.fabiocrameri.ch/colourmaps/)** — Perceptually uniform, colorblind-friendly palettes specifically designed for scientific visualization.
-- **[Datawrapper Blog: Color Guide](https://blog.datawrapper.de/colorguide/)** — Practical guide to choosing and using color in data visualization.
-
-### Key References
-- **[Fundamentals of Data Visualization (Wilke)](https://clauswilke.com/dataviz/)** — Free online book covering principles of effective data visualization; language-agnostic.
-- **[Ten Simple Rules for Better Figures (Rougier et al.)](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833)** — Concise, practical guidelines for publication-ready figures.
+
+| Skill | Description |
+|-------|-------------|
+| [causal-inference-guide](../../skills/analysis/econometrics/causal-inference-guide/) | Causal inference methods including DiD, IV, RDD, and synthetic control |
+| [econml-causal-guide](../../skills/analysis/econometrics/econml-causal-guide/) | Apply EconML for causal inference combining machine learning and econometrics |
+| [iv-regression-guide](../../skills/analysis/econometrics/iv-regression-guide/) | Apply instrumental variables, 2SLS, and address endogeneity issues |
+| [mostly-harmless-guide](../../skills/analysis/econometrics/mostly-harmless-guide/) | Replication code and guide for Mostly Harmless Econometrics methods |
+| [panel-data-analyst](../../skills/analysis/econometrics/panel-data-analyst/) | Expert panel data regression analysis with fixed effects and GMM |
+| [panel-data-guide](../../skills/analysis/econometrics/panel-data-guide/) | Panel data analysis with fixed and random effects models |
+| [python-causality-guide](../../skills/analysis/econometrics/python-causality-guide/) | Learn causal inference with Python using the Brave and True handbook |
+| [robustness-checks](../../skills/analysis/econometrics/robustness-checks/) | Sequential robustness checks in Stata with confounder blocks |
+| [stata-accounting-guide](../../skills/analysis/econometrics/stata-accounting-guide/) | STATA code for empirical accounting and financial economics research |
+| [stata-analyst-guide](../../skills/analysis/econometrics/stata-analyst-guide/) | Stata workflows for publication-ready sociology and social science research |
+| [stata-regression](../../skills/analysis/econometrics/stata-regression/) | Run regression analyses in Stata with publication-ready output |
+| [time-series-guide](../../skills/analysis/econometrics/time-series-guide/) | Apply ARIMA, VAR, cointegration, and time series econometric methods |
+
+
+## Statistics
+
+
+| Skill | Description |
+|-------|-------------|
+| [bayesian-statistics-guide](../../skills/analysis/statistics/bayesian-statistics-guide/) | Bayesian inference methods including prior selection, MCMC, and model comparison |
+| [data-anomaly-detection](../../skills/analysis/statistics/data-anomaly-detection/) | Detect anomalies and outliers in research data using statistical methods |
+| [hypothesis-testing-guide](../../skills/analysis/statistics/hypothesis-testing-guide/) | Statistical hypothesis testing, power analysis, and significance reporting |
+| [meta-analysis-guide](../../skills/analysis/statistics/meta-analysis-guide/) | Conduct systematic meta-analyses with effect size pooling and heterogeneity a... |
+| [ml-experiment-tracker](../../skills/analysis/statistics/ml-experiment-tracker/) | Plan reproducible ML experiment runs with parameters and metrics tracking |
+| [nonparametric-tests-guide](../../skills/analysis/statistics/nonparametric-tests-guide/) | Apply Mann-Whitney, Kruskal-Wallis, and other nonparametric methods |
+| [power-analysis-guide](../../skills/analysis/statistics/power-analysis-guide/) | Sample size calculation and statistical power analysis guide |
+| [pywayne-statistics-guide](../../skills/analysis/statistics/pywayne-statistics-guide/) | 37+ statistical testing methods for rigorous hypothesis testing |
+| [quantitative-methods-guide](../../skills/analysis/statistics/quantitative-methods-guide/) | Design and execute statistical analyses with regression modeling |
+| [sem-guide](../../skills/analysis/statistics/sem-guide/) | Structural equation modeling with latent variables guide |
+| [senior-data-scientist-guide](../../skills/analysis/statistics/senior-data-scientist-guide/) | Statistical modeling, experimentation design, and causal inference |
+| [survival-analysis-guide](../../skills/analysis/statistics/survival-analysis-guide/) | Conduct Kaplan-Meier, Cox regression, and time-to-event analyses |
+
+
+## Wrangling
+
+
+| Skill | Description |
+|-------|-------------|
+| [csv-data-analyzer](../../skills/analysis/wrangling/csv-data-analyzer/) | Load, explore, clean, and analyze CSV data with statistical summaries |
+| [data-cleaning-pipeline](../../skills/analysis/wrangling/data-cleaning-pipeline/) | Systematic data cleaning workflows for research datasets |
+| [data-cog-guide](../../skills/analysis/wrangling/data-cog-guide/) | Upload messy CSVs with minimal prompting for deep automated analysis |
+| [missing-data-handling](../../skills/analysis/wrangling/missing-data-handling/) | Diagnose missing data patterns and apply appropriate imputation strategies |
+| [pandas-data-wrangling](../../skills/analysis/wrangling/pandas-data-wrangling/) | Data cleaning, transformation, and exploratory analysis with pandas |
+| [questionnaire-design-guide](../../skills/analysis/wrangling/questionnaire-design-guide/) | Questionnaire and survey design with Likert scales and coding |
+| [stata-data-cleaning](../../skills/analysis/wrangling/stata-data-cleaning/) | Clean, transform, and validate messy research data using Stata |
+| [survey-data-processing](../../skills/analysis/wrangling/survey-data-processing/) | Clean, recode, and prepare survey response data for analysis |
+| [text-mining-guide](../../skills/analysis/wrangling/text-mining-guide/) | Apply NLP and text mining techniques to research text data |

package/curated/domains/README.md

@@ -1,104 +1,213 @@
-# Curated Domain-Specific Resources
+# Domains — Curated Skills
 
-> Hand-picked resources covering 16 academic domains, each with key tools, databases, and references.
 
-## Computer Science
+> 97 recommended skills for domain-specific research across academic disciplines.
 
-- **[DBLP](https://dblp.org/)** — Comprehensive bibliography of CS publications; clean metadata and open API.
-- **[Papers With Code](https://paperswithcode.com/)** — Links ML/AI papers to code implementations and benchmark leaderboards.
-- **[ACM Digital Library](https://dl.acm.org/)** — Full text of ACM publications plus the Guide to Computing Literature.
-- **[CS Rankings](https://csrankings.org/)** — Metrics-based ranking of CS departments by publication output at top venues.
 
-## AI & Machine Learning
+## Ai Ml
+
+
+| Skill | Description |
+|-------|-------------|
+| [ai-model-benchmarking](../../skills/domains/ai-ml/ai-model-benchmarking/) | Benchmark AI models across 60+ academic evaluation suites and metrics |
+| [annotated-dl-papers-guide](../../skills/domains/ai-ml/annotated-dl-papers-guide/) | Annotated deep learning paper implementations with side-by-side notes |
+| [computer-vision-guide](../../skills/domains/ai-ml/computer-vision-guide/) | Apply computer vision research methods, models, and evaluation tools |
+| [deep-learning-papers-guide](../../skills/domains/ai-ml/deep-learning-papers-guide/) | Annotated deep learning paper implementations with code walkthroughs |
+| [dl-transformer-finetune](../../skills/domains/ai-ml/dl-transformer-finetune/) | Build transformer fine-tuning plans for classification and generation |
+| [generative-ai-guide](../../skills/domains/ai-ml/generative-ai-guide/) | Curated guide to generative AI covering LLMs and diffusion models |
+| [huggingface-inference-guide](../../skills/domains/ai-ml/huggingface-inference-guide/) | Run NLP and CV model inference via Hugging Face free-tier API |
+| [keras-deep-learning](../../skills/domains/ai-ml/keras-deep-learning/) | Build and debug deep learning models with Keras and TensorFlow backend |
+| [llm-evaluation-guide](../../skills/domains/ai-ml/llm-evaluation-guide/) | Evaluate and benchmark large language models for research applications |
+| [llm-from-scratch-guide](../../skills/domains/ai-ml/llm-from-scratch-guide/) | Build a ChatGPT-like LLM from scratch using PyTorch step by step |
+| [ml-pipeline-guide](../../skills/domains/ai-ml/ml-pipeline-guide/) | Build and deploy reproducible production ML pipelines for research |
+| [nlp-toolkit-guide](../../skills/domains/ai-ml/nlp-toolkit-guide/) | NLP analysis with perplexity scoring, burstiness, and entropy metrics |
+| [prompt-engineering-research](../../skills/domains/ai-ml/prompt-engineering-research/) | Systematic prompt engineering methods for AI-assisted academic research workf... |
+| [pytorch-guide](../../skills/domains/ai-ml/pytorch-guide/) | Avoid common PyTorch mistakes and apply robust training patterns |
+| [pytorch-lightning-guide](../../skills/domains/ai-ml/pytorch-lightning-guide/) | PyTorch Lightning framework for scalable model training and research |
+| [reinforcement-learning-guide](../../skills/domains/ai-ml/reinforcement-learning-guide/) | Reinforcement learning fundamentals, algorithms, and research |
+| [tensorflow-guide](../../skills/domains/ai-ml/tensorflow-guide/) | TensorFlow best practices for tf.function, GPU memory, and deployment |
+| [transformer-architecture-guide](../../skills/domains/ai-ml/transformer-architecture-guide/) | Guide to Transformer architectures for NLP and computer vision |
 
-- **[Hugging Face](https://huggingface.co/)** — Open platform for models, datasets, and spaces; the hub of open-source AI.
-- **[arXiv cs.AI / cs.LG](https://arxiv.org/list/cs.AI/recent)** — Daily preprints in artificial intelligence and machine learning.
-- **[Distill.pub](https://distill.pub/)** — Clear, interactive explanations of machine learning concepts (archived but invaluable).
-- **[Awesome Machine Learning](https://github.com/josephmisiti/awesome-machine-learning)** — Curated list of ML frameworks, libraries, and tools across languages.
 
 ## Biomedical
 
-- **[PubMed / MEDLINE](https://pubmed.ncbi.nlm.nih.gov/)** — Authoritative index of biomedical literature with MeSH-controlled vocabulary.
-- **[UniProt](https://www.uniprot.org/)** — Comprehensive protein sequence and functional annotation database.
-- **[NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/)** — Public repository for high-throughput gene expression and genomics datasets.
-- **[BioRender](https://www.biorender.com/)** — Scientific illustration tool with thousands of pre-made biology icons and templates.
+
+| Skill | Description |
+|-------|-------------|
+| [bioagents-guide](../../skills/domains/biomedical/bioagents-guide/) | AI scientist framework for autonomous biological research workflows |
+| [clinical-research-guide](../../skills/domains/biomedical/clinical-research-guide/) | Design clinical studies and report using CONSORT, STROBE guidelines |
+| [clinicaltrials-api](../../skills/domains/biomedical/clinicaltrials-api/) | Clinical trial registry database search API |
+| [epidemiology-guide](../../skills/domains/biomedical/epidemiology-guide/) | Epidemiological study designs, measures of association, and public health ana... |
+| [genomics-analysis-guide](../../skills/domains/biomedical/genomics-analysis-guide/) | Workflows for RNA-seq, GWAS, and variant calling in genomic research |
+| [medgeclaw-guide](../../skills/domains/biomedical/medgeclaw-guide/) | AI research assistant for biomedicine, RNA-seq, and drug discovery |
+| [medical-imaging-guide](../../skills/domains/biomedical/medical-imaging-guide/) | Medical image analysis with deep learning for research applications |
+
+
+## Business
+
+
+| Skill | Description |
+|-------|-------------|
+| [architecture-design-guide](../../skills/domains/business/architecture-design-guide/) | Design principles of form, function, sustainability in architecture |
+| [innovation-management-guide](../../skills/domains/business/innovation-management-guide/) | Innovation metrics, R&D management research, and technology forecasting |
+| [market-analysis-guide](../../skills/domains/business/market-analysis-guide/) | Structured frameworks for market sizing, competitive analysis, and strategic ... |
+| [operations-research-guide](../../skills/domains/business/operations-research-guide/) | Optimization and operations research methods for business and logistics |
+| [strategic-management-guide](../../skills/domains/business/strategic-management-guide/) | Frameworks for strategic planning, resource allocation, and organizational an... |
+
 
 ## Chemistry
 
-- **[PubChem](https://pubchem.ncbi.nlm.nih.gov/)** — Open chemistry database with compound, substance, and bioassay data (110M+ compounds).
-- **[RDKit](https://www.rdkit.org/)** — Open-source cheminformatics toolkit for molecular manipulation and descriptor calculation.
-- **[Reaxys](https://www.reaxys.com/)** — Elsevier's curated reaction and substance database for synthetic chemistry.
-- **[ChemRxiv](https://chemrxiv.org/)** — Preprint server for chemistry from ACS, RSC, and GDCh.
 
-## Economics
+| Skill | Description |
+|-------|-------------|
+| [computational-chemistry-guide](../../skills/domains/chemistry/computational-chemistry-guide/) | DFT, molecular simulation, and reaction prediction tools for chemists |
+| [molecular-dynamics-guide](../../skills/domains/chemistry/molecular-dynamics-guide/) | Molecular dynamics simulation setup, execution, and trajectory analysis |
+| [pubchem-api-guide](../../skills/domains/chemistry/pubchem-api-guide/) | Search PubChem for chemical compounds, structures, and bioassay data |
+| [retrosynthesis-guide](../../skills/domains/chemistry/retrosynthesis-guide/) | Retrosynthetic analysis and computational reaction prediction |
+| [spectroscopy-analysis-guide](../../skills/domains/chemistry/spectroscopy-analysis-guide/) | Spectral data analysis for NMR, IR, mass spectrometry, and UV-Vis |
 
-- **[NBER Working Papers](https://www.nber.org/papers)** — Influential working paper series covering all areas of economics.
-- **[FRED (Federal Reserve Economic Data)](https://fred.stlouisfed.org/)** — 800,000+ economic time series; essential for macroeconomic research.
-- **[AEA RCT Registry](https://www.socialscienceregistry.org/)** — Registry for randomized controlled trials in economics and social science.
-- **[RePEc / IDEAS](https://ideas.repec.org/)** — Largest open bibliographic database for economics with rankings and author profiles.
 
-## Finance
+## Cs
 
-- **[WRDS](https://wrds-www.wharton.upenn.edu/)** — Wharton Research Data Services; gateway to CRSP, Compustat, and other finance databases.
-- **[Ken French Data Library](https://mba.tuck.dartmouth.edu/pages/faculty/ken.french/data_library.html)** — Factor portfolios and returns data; essential for asset pricing research.
-- **[QuantLib](https://www.quantlib.org/)** — Open-source library for quantitative finance: derivatives pricing, risk management.
 
-## Law
+| Skill | Description |
+|-------|-------------|
+| [algorithms-complexity-guide](../../skills/domains/cs/algorithms-complexity-guide/) | Analyze algorithm complexity and computational efficiency for research |
+| [dblp-api](../../skills/domains/cs/dblp-api/) | Search computer science publications, authors, and venues via DBLP |
+| [distributed-systems-guide](../../skills/domains/cs/distributed-systems-guide/) | Distributed systems design patterns and analysis for CS research |
+| [formal-verification-guide](../../skills/domains/cs/formal-verification-guide/) | Formal methods, theorem proving, and model checking for CS research |
+| [software-engineering-research](../../skills/domains/cs/software-engineering-research/) | Guide to software engineering research topics and methodologies |
 
-- **[Google Scholar Case Law](https://scholar.google.com/scholar?q=&hl=en&as_sdt=4)** — Free search of US case law and legal journals.
-- **[SSRN Legal Scholarship Network](https://www.ssrn.com/index.cfm/en/lsn/)** — Preprints and working papers across all legal disciplines.
-- **[CourtListener (Free Law Project)](https://www.courtlistener.com/)** — Free, open archive of US court opinions, oral arguments, and judicial data.
 
-## Social Science
+## Ecology
+
+
+| Skill | Description |
+|-------|-------------|
+| [biodiversity-data-guide](../../skills/domains/ecology/biodiversity-data-guide/) | Biodiversity data access, species occurrence, and ecological tools |
+| [conservation-biology-guide](../../skills/domains/ecology/conservation-biology-guide/) | Apply conservation biology methods, databases, and assessment tools |
+| [gbif-api](../../skills/domains/ecology/gbif-api/) | Global biodiversity data API for species occurrences and datasets |
+| [inaturalist-api](../../skills/domains/ecology/inaturalist-api/) | Citizen science platform API for biodiversity observations |
+| [species-distribution-guide](../../skills/domains/ecology/species-distribution-guide/) | Species distribution modeling with MaxEnt, SDM methods, and GBIF data |
+
+
+## Economics
+
+
+| Skill | Description |
+|-------|-------------|
+| [behavioral-economics-guide](../../skills/domains/economics/behavioral-economics-guide/) | Behavioral economics research methods and key frameworks |
+| [development-economics-guide](../../skills/domains/economics/development-economics-guide/) | Apply development economics research methods and data sources |
+| [fred-api](../../skills/domains/economics/fred-api/) | Federal Reserve Economic Data API for US economic indicators |
+| [imf-data-api-guide](../../skills/domains/economics/imf-data-api-guide/) | Retrieve IMF economic indicators, exchange rates, and country data |
+| [post-labor-economics](../../skills/domains/economics/post-labor-economics/) | Post-labor economies with automation, UBI, and wealth distribution |
+| [pricing-psychology-guide](../../skills/domains/economics/pricing-psychology-guide/) | Behavioral economics in pricing strategies and consumer decisions |
+| [world-bank-data-guide](../../skills/domains/economics/world-bank-data-guide/) | Access World Bank development indicators and country statistics |
 
-- **[ICPSR](https://www.icpsr.umich.edu/)** — Largest archive of social science data; 16,000+ datasets with documentation.
-- **[Qualtrics](https://www.qualtrics.com/)** — Survey platform widely used in social science research; free academic accounts available.
-- **[World Values Survey](https://www.worldvaluessurvey.org/)** — Cross-national time-series survey of human beliefs and values (120+ countries).
 
 ## Education
 
-- **[ERIC](https://eric.ed.gov/)** — IES-sponsored database of education research and information.
-- **[OECD Education Data](https://data.oecd.org/education.htm)** — International education statistics and indicators from OECD countries.
-- **[What Works Clearinghouse](https://ies.ed.gov/ncee/wwc/)** — Evidence reviews of education programs, policies, and practices.
 
-## Physics
+| Skill | Description |
+|-------|-------------|
+| [assessment-design-guide](../../skills/domains/education/assessment-design-guide/) | Psychometrics and educational assessment design for researchers |
+| [curriculum-design-guide](../../skills/domains/education/curriculum-design-guide/) | Systematic approaches to curriculum design using backward design and alignment |
+| [educational-research-methods](../../skills/domains/education/educational-research-methods/) | Quantitative and qualitative research methods for education studies |
+| [learning-science-guide](../../skills/domains/education/learning-science-guide/) | Evidence-based learning science principles for educational research and practice |
+| [mooc-analytics-guide](../../skills/domains/education/mooc-analytics-guide/) | Analyzing MOOC data, learning analytics, and online education metrics |
 
-- **[arXiv Physics](https://arxiv.org/archive/physics)** — Preprint server that physicists have used since 1991; the original open access platform.
-- **[INSPIRE-HEP](https://inspirehep.net/)** — High-energy physics literature database with citation analysis and author disambiguation.
-- **[NIST Physical Reference Data](https://www.nist.gov/pml/productsservices/physical-reference-data)** — Fundamental physical constants, atomic spectra, and reference datasets.
 
-## Ecology & Environmental Science
+## Finance
 
-- **[GBIF](https://www.gbif.org/)** — Global Biodiversity Information Facility; 2B+ occurrence records for biodiversity research.
-- **[NASA Earthdata](https://earthdata.nasa.gov/)** — Free access to NASA's Earth observation data across atmosphere, land, and ocean.
-- **[Movebank](https://www.movebank.org/)** — Free platform for managing, sharing, and analyzing animal movement data.
 
-## Mathematics
+| Skill | Description |
+|-------|-------------|
+| [financial-data-analysis](../../skills/domains/finance/financial-data-analysis/) | Methods for acquiring, cleaning, and analyzing financial datasets for research |
+| [portfolio-optimization-guide](../../skills/domains/finance/portfolio-optimization-guide/) | Portfolio theory, optimization algorithms, and asset allocation methods |
+| [quantitative-finance-guide](../../skills/domains/finance/quantitative-finance-guide/) | Quantitative methods for financial modeling, derivatives pricing, and risk an... |
+| [risk-modeling-guide](../../skills/domains/finance/risk-modeling-guide/) | Financial risk modeling including VaR, stress testing, and credit risk |
+| [stata-accounting-research](../../skills/domains/finance/stata-accounting-research/) | STATA code patterns for empirical accounting and finance research |
+
+
+## Geoscience
+
+
+| Skill | Description |
+|-------|-------------|
+| [climate-modeling-guide](../../skills/domains/geoscience/climate-modeling-guide/) | Climate simulation, modeling tools, and climate data analysis methods |
+| [climate-science-guide](../../skills/domains/geoscience/climate-science-guide/) | Climate data analysis, modeling workflows, and carbon neutrality research met... |
+| [gis-remote-sensing-guide](../../skills/domains/geoscience/gis-remote-sensing-guide/) | GIS analysis and remote sensing workflows for geospatial research applications |
+| [satellite-remote-sensing](../../skills/domains/geoscience/satellite-remote-sensing/) | Satellite imagery analysis and remote sensing for earth science research |
+| [seismology-data-guide](../../skills/domains/geoscience/seismology-data-guide/) | Earthquake data analysis, seismogram processing, and seismic research |
 
-- **[MathSciNet](https://mathscinet.ams.org/)** — AMS's comprehensive reviews and bibliography database for mathematics.
-- **[OEIS](https://oeis.org/)** — The On-Line Encyclopedia of Integer Sequences; indispensable for combinatorics and number theory.
-- **[Lean Community](https://leanprover-community.github.io/)** — Resources for the Lean proof assistant and Mathlib library; growing role in formalized math.
 
 ## Humanities
 
-- **[JSTOR](https://www.jstor.org/)** — Digital library of academic journals, books, and primary sources; strong humanities coverage.
-- **[HathiTrust Digital Library](https://www.hathitrust.org/)** — 17M+ digitized volumes from major research libraries; full-text search for public domain works.
-- **[Project Gutenberg](https://www.gutenberg.org/)** — 70,000+ free eBooks; essential primary source collection for literary and historical research.
 
-## Business & Management
+| Skill | Description |
+|-------|-------------|
+| [digital-humanities-guide](../../skills/domains/humanities/digital-humanities-guide/) | Computational methods for humanities research including text mining and netwo... |
+| [ethical-philosophy-guide](../../skills/domains/humanities/ethical-philosophy-guide/) | Applied ethics research methods and major ethical frameworks |
+| [history-research-guide](../../skills/domains/humanities/history-research-guide/) | Historical research from primary sources to scholarly analysis |
+| [philosophy-research-guide](../../skills/domains/humanities/philosophy-research-guide/) | Research methods and analytical frameworks for philosophical inquiry and scho... |
+| [political-history-guide](../../skills/domains/humanities/political-history-guide/) | Chinese and European political struggle history and comparative analysis |
 
-- **[Harvard Business Review](https://hbr.org/)** — Practitioner-oriented management research and case studies.
-- **[ABI/INFORM (ProQuest)](https://about.proquest.com/en/products-services/abi_inform_complete/)** — Comprehensive business database covering journals, dissertations, and trade publications.
-- **[Crunchbase](https://www.crunchbase.com/)** — Company, funding, and investor data; widely used in entrepreneurship and innovation research.
 
-## Pharmaceutical Science
+## Law
 
-- **[DrugBank](https://go.drugbank.com/)** — Comprehensive database of drug and drug target information.
-- **[ClinicalTrials.gov](https://clinicaltrials.gov/)** — Registry of clinical studies conducted worldwide; 400,000+ studies.
-- **[ChEMBL](https://www.ebi.ac.uk/chembl/)** — Open bioactivity database of drug-like compounds; curated from medicinal chemistry literature.
 
-## Geoscience
+| Skill | Description |
+|-------|-------------|
+| [courtlistener-api](../../skills/domains/law/courtlistener-api/) | Legal case law database with PACER data and judge profiles |
+| [legal-nlp-guide](../../skills/domains/law/legal-nlp-guide/) | NLP techniques for legal text analysis, case law mining, and contracts |
+| [legal-research-guide](../../skills/domains/law/legal-research-guide/) | Legal research methods, case law analysis, and compliance tools |
+| [patent-analysis-guide](../../skills/domains/law/patent-analysis-guide/) | Patent search, classification, landscape analysis, and prior art mining |
+| [regulatory-compliance-guide](../../skills/domains/law/regulatory-compliance-guide/) | Regulatory text mining, compliance research, and policy analysis tools |
+
+
+## Math
+
+
+| Skill | Description |
+|-------|-------------|
+| [linear-algebra-applications](../../skills/domains/math/linear-algebra-applications/) | Apply linear algebra concepts to research computing and data analysis |
+| [numerical-methods-guide](../../skills/domains/math/numerical-methods-guide/) | Apply numerical methods and scientific computing techniques |
+| [oeis-api](../../skills/domains/math/oeis-api/) | On-Line Encyclopedia of Integer Sequences API |
+| [symbolic-computation-guide](../../skills/domains/math/symbolic-computation-guide/) | Computer algebra systems: SymPy, SageMath, and Mathematica for research |
+| [topology-data-analysis](../../skills/domains/math/topology-data-analysis/) | Topological data analysis: persistent homology, Mapper, and TDA tools |
+
+
+## Pharma
+
+
+| Skill | Description |
+|-------|-------------|
+| [clinical-pharmacology-guide](../../skills/domains/pharma/clinical-pharmacology-guide/) | Clinical pharmacology principles for dosing, drug interactions, and patient s... |
+| [clinical-trial-design-guide](../../skills/domains/pharma/clinical-trial-design-guide/) | Clinical trial methodology, biostatistics, and study design guidance |
+| [drug-development-guide](../../skills/domains/pharma/drug-development-guide/) | End-to-end drug development pipeline from target identification to regulatory... |
+| [drug-target-interaction](../../skills/domains/pharma/drug-target-interaction/) | Computational drug-target interaction prediction and virtual screening |
+| [pharmacovigilance-guide](../../skills/domains/pharma/pharmacovigilance-guide/) | Adverse drug event detection, safety signal mining, and drug monitoring |
+
+
+## Physics
+
+
+| Skill | Description |
+|-------|-------------|
+| [astrophysics-data-guide](../../skills/domains/physics/astrophysics-data-guide/) | Astronomical data processing with Astropy, FITS files, and sky surveys |
+| [computational-physics-guide](../../skills/domains/physics/computational-physics-guide/) | Computational physics methods, simulations, and research tools |
+| [nasa-ads-api](../../skills/domains/physics/nasa-ads-api/) | Search astrophysics and physics literature via NASA ADS bibliographic database |
+| [particle-physics-guide](../../skills/domains/physics/particle-physics-guide/) | Particle physics data analysis with ROOT, HEPData, and event processing |
+| [quantum-computing-guide](../../skills/domains/physics/quantum-computing-guide/) | Explore quantum computing research with Qiskit and Cirq frameworks |
+
+
+## Social Science
+
 
-- **[USGS Publications](https://pubs.usgs.gov/)** — Free access to all US Geological Survey scientific publications and data.
-- **[Pangaea](https://www.pangaea.de/)** — Open-access repository for earth and environmental science data.
-- **[GeoRef (AGI)](https://www.americangeosciences.org/georef)** — Comprehensive bibliographic database for the geosciences (4M+ references).
+| Skill | Description |
+|-------|-------------|
+| [network-analysis-guide](../../skills/domains/social-science/network-analysis-guide/) | Social network analysis methods, metrics, and visualization tools |
+| [psychology-research-guide](../../skills/domains/social-science/psychology-research-guide/) | Psychological research methods, experimental design, and analysis |
+| [social-research-methods](../../skills/domains/social-science/social-research-methods/) | Core methods for empirical social science research including surveys and expe... |
+| [sociology-research-guide](../../skills/domains/social-science/sociology-research-guide/) | Sociological thinking from observations to rigorous research design |
+| [survey-research-guide](../../skills/domains/social-science/survey-research-guide/) | Design, deploy, and analyze surveys for social science and organizational res... |