@wentorai/research-plugins 1.0.0 → 1.2.0

package/curated/literature/README.md

@@ -1,53 +1,122 @@
-# Curated Literature Resources
+# Literature — Curated Skills
 
-> Hand-picked resources for academic researchers working with literature search, discovery, and management.
 
-## Search
+> 89 recommended skills for finding, discovering, and managing academic literature.
 
-### Tools & Software
-- **[Google Scholar](https://scholar.google.com/)** — The most widely used academic search engine; covers journals, theses, books, and patents across all disciplines.
-- **[Semantic Scholar](https://www.semanticscholar.org/)** — AI-powered search engine from AI2 with TLDR summaries, citation context, and influence scores.
-- **[OpenAlex](https://openalex.org/)** — Free, open catalog of the global research system (replaces Microsoft Academic); full API access for bibliometric analysis.
-- **[Dimensions](https://www.dimensions.ai/)** — Linked research knowledge system connecting publications, grants, patents, datasets, and clinical trials.
-- **[Connected Papers](https://www.connectedpapers.com/)** — Visual graph tool that builds a similarity network around a seed paper to find related work.
-- **[PubMed](https://pubmed.ncbi.nlm.nih.gov/)** — NCBI's authoritative database for biomedical and life sciences literature (35M+ citations).
-- **[Web of Science](https://www.webofscience.com/)** — Clarivate's curated citation index; gold standard for impact metrics (JIF, ESI).
-- **[Scopus](https://www.scopus.com/)** — Elsevier's abstract and citation database; broader journal coverage than WoS in some fields.
 
-### Key References
-- **[The Lens](https://www.lens.org/)** — Free scholarly and patent search with open data linking; great for innovation mapping.
-- **[CORE](https://core.ac.uk/)** — Aggregates open access research outputs from repositories and journals worldwide (200M+ records).
 
 ## Discovery
 
-### Tools & Software
-- **[Research Rabbit](https://www.researchrabbit.ai/)** — Free tool that recommends papers based on your collections; "Spotify for papers."
-- **[Elicit](https://elicit.com/)** — AI research assistant that finds relevant papers, extracts claims, and summarizes findings.
-- **[Litmaps](https://www.litmaps.com/)** — Dynamic citation mapping that visualizes how papers connect over time; automatic update alerts.
-- **[Google Scholar Alerts](https://scholar.google.com/scholar_alerts)** — Email notifications for new papers matching your keywords or citing your work.
-
-### Key References
-- **[Inciteful](https://inciteful.xyz/)** — Build a network of papers from a seed article; identify important but overlooked connections.
-
-## Fulltext Access
-
-### Tools & Software
-- **[Unpaywall](https://unpaywall.org/)** — Browser extension that finds legal free full-text PDFs via open access repositories (20M+ articles).
-- **[CORE Discovery](https://core.ac.uk/services/discovery)** — Browser extension to find free OA copies of paywalled articles.
-- **[Open Access Button](https://openaccessbutton.org/)** — Locates free legal copies or requests them directly from authors.
-
-### Preprint Servers
-- **[arXiv](https://arxiv.org/)** — The foundational preprint server for physics, math, CS, and quantitative biology.
-- **[bioRxiv](https://www.biorxiv.org/)** — Preprint server for the biological sciences, operated by Cold Spring Harbor Laboratory.
-- **[SSRN](https://www.ssrn.com/)** — Leading preprint platform for social sciences, economics, and law.
-- **[OSF Preprints](https://osf.io/preprints/)** — Aggregator across 30+ preprint services; part of the Open Science Framework.
-
-## Metadata & Metrics
-
-### Tools & Software
-- **[DOI.org](https://www.doi.org/)** — Resolve any DOI to its metadata and landing page.
-- **[Crossref](https://www.crossref.org/)** — Open metadata API for 140M+ records; the backbone of scholarly linking.
-- **[OpenCitations](https://opencitations.net/)** — Open citation data (COCI index); free alternative to proprietary citation databases.
-- **[Altmetric](https://www.altmetric.com/)** — Tracks attention to research across social media, news, policy, and patents.
-- **[Scimago Journal Rank (SJR)](https://www.scimagojr.com/)** — Free journal ranking and visualization portal based on Scopus data.
-- **[CoCites](https://www.cocites.com/)** — Co-citation analysis tool to find the most relevant papers in any field cluster.
+
+| Skill | Description |
+|-------|-------------|
+| [arxiv-paper-monitoring](../../skills/literature/discovery/arxiv-paper-monitoring/) | Set up automated monitoring for new arXiv papers in your research area |
+| [citation-alert-guide](../../skills/literature/discovery/citation-alert-guide/) | Set up citation alerts and track new papers citing key references |
+| [conference-proceedings-guide](../../skills/literature/discovery/conference-proceedings-guide/) | Find, access, and cite conference papers and proceedings effectively |
+| [literature-mapping-guide](../../skills/literature/discovery/literature-mapping-guide/) | Visual literature mapping and connected papers exploration |
+| [paper-recommendation-guide](../../skills/literature/discovery/paper-recommendation-guide/) | Systematic paper recommendation and discovery using multiple methods |
+| [paper-tracking-guide](../../skills/literature/discovery/paper-tracking-guide/) | Track new publications via RSS, alerts, and citation notifications |
+| [papers-we-love-guide](../../skills/literature/discovery/papers-we-love-guide/) | Community-curated directory of influential CS research papers |
+| [rss-paper-feeds](../../skills/literature/discovery/rss-paper-feeds/) | Set up RSS feeds and alerts to track new publications in your research area |
+| [semantic-paper-radar](../../skills/literature/discovery/semantic-paper-radar/) | Semantic literature discovery and synthesis using embeddings |
+| [semantic-scholar-recs-guide](../../skills/literature/discovery/semantic-scholar-recs-guide/) | Using Semantic Scholar recommendations API for paper discovery |
+| [zotero-arxiv-daily-guide](../../skills/literature/discovery/zotero-arxiv-daily-guide/) | Guide to Zotero arXiv Daily for personalized daily paper recommendations |
+
+
+## Fulltext
+
+
+| Skill | Description |
+|-------|-------------|
+| [bioc-pmc-api](../../skills/literature/fulltext/bioc-pmc-api/) | Access PMC Open Access articles in BioC format for text mining |
+| [core-api-guide](../../skills/literature/fulltext/core-api-guide/) | Search and retrieve open access research papers via CORE aggregator |
+| [dataverse-api](../../skills/literature/fulltext/dataverse-api/) | Deposit and discover research datasets via Harvard Dataverse API |
+| [doaj-api](../../skills/literature/fulltext/doaj-api/) | Search open access journals and articles in the DOAJ directory |
+| [hal-archive-api](../../skills/literature/fulltext/hal-archive-api/) | Access French and European research via the HAL open archive API |
+| [institutional-repository-guide](../../skills/literature/fulltext/institutional-repository-guide/) | Access papers from institutional and subject repositories at scale |
+| [interlibrary-loan-guide](../../skills/literature/fulltext/interlibrary-loan-guide/) | Access papers through interlibrary loan and document delivery services |
+| [open-access-guide](../../skills/literature/fulltext/open-access-guide/) | Navigate open access policies, repositories, and legal full-text retrieval me... |
+| [open-access-mining-guide](../../skills/literature/fulltext/open-access-mining-guide/) | Mine open access full-text repositories for research data extraction |
+| [osf-api](../../skills/literature/fulltext/osf-api/) | Manage open science projects and preprints via the OSF REST API |
+| [pmc-ftp-bulk-download](../../skills/literature/fulltext/pmc-ftp-bulk-download/) | Bulk download PMC Open Access articles via FTP for large-scale mining |
+| [pmc-oai-api](../../skills/literature/fulltext/pmc-oai-api/) | PubMed Central OAI-PMH metadata harvesting |
+| [preprint-servers-guide](../../skills/literature/fulltext/preprint-servers-guide/) | Guide to preprint servers across scientific disciplines |
+| [unpaywall-api](../../skills/literature/fulltext/unpaywall-api/) | Find free legal full-text versions of scholarly articles via Unpaywall |
+| [zotero-ai-butler-guide](../../skills/literature/fulltext/zotero-ai-butler-guide/) | AI-powered paper summarization plugin for Zotero |
+| [zotero-scihub-guide](../../skills/literature/fulltext/zotero-scihub-guide/) | Zotero plugin for automatic PDF retrieval from Sci-Hub |
+
+
+## Metadata
+
+
+| Skill | Description |
+|-------|-------------|
+| [academic-paper-summarizer](../../skills/literature/metadata/academic-paper-summarizer/) | Summarize academic papers with structured extraction of key elements |
+| [altmetrics-guide](../../skills/literature/metadata/altmetrics-guide/) | Guide to altmetrics and research impact beyond traditional citations |
+| [bibliometrix-guide](../../skills/literature/metadata/bibliometrix-guide/) | Perform science mapping and bibliometric analysis with R bibliometrix |
+| [citation-network-guide](../../skills/literature/metadata/citation-network-guide/) | Analyze citation networks, impact metrics, and bibliometric patterns |
+| [crossref-api](../../skills/literature/metadata/crossref-api/) | Resolve DOIs and retrieve publication metadata from CrossRef registry |
+| [crossref-event-data-api](../../skills/literature/metadata/crossref-event-data-api/) | Track scholarly mentions across the web via Crossref Event Data |
+| [datacite-api](../../skills/literature/metadata/datacite-api/) | Resolve dataset DOIs and query research data metadata via DataCite |
+| [doi-content-negotiation](../../skills/literature/metadata/doi-content-negotiation/) | Retrieve structured metadata from any DOI via HTTP content negotiation |
+| [doi-resolution-guide](../../skills/literature/metadata/doi-resolution-guide/) | DOI content negotiation and metadata retrieval techniques |
+| [h-index-guide](../../skills/literature/metadata/h-index-guide/) | Understanding and calculating research impact metrics |
+| [journal-metrics-guide](../../skills/literature/metadata/journal-metrics-guide/) | Understand journal impact factors, h5-index, CiteScore, and SJR |
+| [opencitations-api](../../skills/literature/metadata/opencitations-api/) | Query open citation data and reference networks via OpenCitations |
+| [orcid-api](../../skills/literature/metadata/orcid-api/) | Look up researcher profiles and academic identities via the ORCID registry |
+| [orcid-integration-guide](../../skills/literature/metadata/orcid-integration-guide/) | Set up and leverage ORCID for researcher identification and profiles |
+| [orkg-api](../../skills/literature/metadata/orkg-api/) | Query the Open Research Knowledge Graph for structured research data |
+| [plumx-metrics-api](../../skills/literature/metadata/plumx-metrics-api/) | Track research impact beyond citations via PlumX altmetrics API |
+| [ror-organization-api](../../skills/literature/metadata/ror-organization-api/) | Identify and link research organizations via the ROR registry API |
+| [sophosia-reference-guide](../../skills/literature/metadata/sophosia-reference-guide/) | Reference manager with PDF viewer and Markdown note support |
+| [viaf-authority-api](../../skills/literature/metadata/viaf-authority-api/) | Disambiguate author identities via the VIAF authority file API |
+| [wikidata-api-guide](../../skills/literature/metadata/wikidata-api-guide/) | Query Wikidata SPARQL for scholarly metadata, authors, and entities |
+| [zoplicate-dedup-guide](../../skills/literature/metadata/zoplicate-dedup-guide/) | Detect and manage duplicate items in Zotero libraries |
+| [zotero-actions-tags-guide](../../skills/literature/metadata/zotero-actions-tags-guide/) | Zotero workflow automation with custom actions and tags |
+| [zotmoov-guide](../../skills/literature/metadata/zotmoov-guide/) | Zotero plugin for automatic attachment file organization |
+| [zutilo-guide](../../skills/literature/metadata/zutilo-guide/) | Zotero utility plugin for keyboard shortcuts and batch editing |
+
+
+## Search
+
+
+| Skill | Description |
+|-------|-------------|
+| [arxiv-api](../../skills/literature/search/arxiv-api/) | Search and retrieve preprints from the arXiv open-access repository |
+| [arxiv-batch-reporting](../../skills/literature/search/arxiv-batch-reporting/) | Batch search and report generation from arXiv preprint repository |
+| [arxiv-cli-tools](../../skills/literature/search/arxiv-cli-tools/) | Command-line tools for searching and batch-downloading arXiv papers |
+| [arxiv-osiris](../../skills/literature/search/arxiv-osiris/) | Search and download arXiv papers via Python and PowerShell scripts |
+| [arxiv-paper-processor](../../skills/literature/search/arxiv-paper-processor/) | Process and analyze arXiv papers systematically for research workflows |
+| [baidu-scholar-guide](../../skills/literature/search/baidu-scholar-guide/) | Using Baidu Scholar for Chinese and English academic literature search |
+| [base-academic-search](../../skills/literature/search/base-academic-search/) | Search 400M+ open access documents via the BASE search engine API |
+| [biorxiv-api](../../skills/literature/search/biorxiv-api/) | Preprint server API for biology and medicine papers |
+| [boolean-search-guide](../../skills/literature/search/boolean-search-guide/) | Master Boolean operators and advanced search syntax for academic databases |
+| [chatpaper-guide](../../skills/literature/search/chatpaper-guide/) | Use ChatPaper to summarize and search arXiv papers with LLM assistance |
+| [citation-chaining-guide](../../skills/literature/search/citation-chaining-guide/) | Forward and backward citation chaining techniques for literature search |
+| [citeseerx-api](../../skills/literature/search/citeseerx-api/) | Search computer science literature via the CiteSeerX digital library |
+| [database-comparison-guide](../../skills/literature/search/database-comparison-guide/) | Compare major academic databases and when to use each for research |
+| [deep-literature-search](../../skills/literature/search/deep-literature-search/) | Multi-source exhaustive literature search across academic databases |
+| [deepgit-search-guide](../../skills/literature/search/deepgit-search-guide/) | Deep research tool for discovering academic code in Git repositories |
+| [eric-education-api](../../skills/literature/search/eric-education-api/) | Search 2M+ education research records via the ERIC database API |
+| [europe-pmc-api](../../skills/literature/search/europe-pmc-api/) | Search biomedical and life sciences literature via Europe PMC |
+| [findpapers-guide](../../skills/literature/search/findpapers-guide/) | Search multiple academic databases simultaneously with Findpapers |
+| [google-scholar-guide](../../skills/literature/search/google-scholar-guide/) | Advanced Google Scholar search techniques for comprehensive literature discovery |
+| [ieee-xplore-api](../../skills/literature/search/ieee-xplore-api/) | Search IEEE's 6M+ engineering and CS publications via the Xplore API |
+| [lens-scholarly-api](../../skills/literature/search/lens-scholarly-api/) | Search 300M+ scholarly and patent records via the Lens.org API |
+| [mesh-terms-guide](../../skills/literature/search/mesh-terms-guide/) | Navigate MeSH vocabulary for precise PubMed and MEDLINE searches |
+| [multi-database-literature-search](../../skills/literature/search/multi-database-literature-search/) | Conduct comprehensive literature searches across multiple academic databases |
+| [open-library-api](../../skills/literature/search/open-library-api/) | Search and access book metadata via the Open Library API |
+| [open-semantic-search-guide](../../skills/literature/search/open-semantic-search-guide/) | Self-hosted semantic search and text mining platform |
+| [openaire-api](../../skills/literature/search/openaire-api/) | Search EU-funded research outputs via the OpenAIRE Graph API |
+| [openalex-api](../../skills/literature/search/openalex-api/) | Query the OpenAlex catalog of scholarly works, authors, and institutions |
+| [paper-search-mcp-guide](../../skills/literature/search/paper-search-mcp-guide/) | MCP server for searching papers across arXiv, PubMed, bioRxiv |
+| [papers-chat-guide](../../skills/literature/search/papers-chat-guide/) | Conversational interface for querying and discussing papers |
+| [pasa-paper-search-guide](../../skills/literature/search/pasa-paper-search-guide/) | Advanced paper search agent powered by LLMs for literature discovery |
+| [plos-open-access-api](../../skills/literature/search/plos-open-access-api/) | Search PLOS open access journals with full-text Solr-powered API |
+| [pubmed-api](../../skills/literature/search/pubmed-api/) | Search biomedical literature and retrieve records via PubMed E-utilities |
+| [scielo-api](../../skills/literature/search/scielo-api/) | Access Latin American and developing world research via SciELO API |
+| [scientify-literature-survey](../../skills/literature/search/scientify-literature-survey/) | Search, filter, download and cluster academic papers on a topic |
+| [semantic-scholar-api](../../skills/literature/search/semantic-scholar-api/) | Search papers and analyze citation graphs via Semantic Scholar |
+| [share-research-api](../../skills/literature/search/share-research-api/) | Discover open access research outputs via the SHARE notification API |
+| [systematic-search-strategy](../../skills/literature/search/systematic-search-strategy/) | Construct rigorous systematic search strategies for literature reviews |
+| [worldcat-search-api](../../skills/literature/search/worldcat-search-api/) | Search the world's largest library catalog via OCLC WorldCat API |

package/curated/research/README.md

@@ -1,62 +1,110 @@
-# Curated Research Methods Resources
+# Research — Curated Skills
+
+
+> 70 recommended skills for research methodology, deep research, peer review, and automation.
+
+
+
+## Automation
+
+
+| Skill | Description |
+|-------|-------------|
+| [ai-scientist-guide](../../skills/research/automation/ai-scientist-guide/) | End-to-end automated scientific discovery with AI Scientist v2 |
+| [ai-scientist-v2-guide](../../skills/research/automation/ai-scientist-v2-guide/) | Automated scientific discovery via agentic tree search by Sakana AI |
+| [aim-experiment-guide](../../skills/research/automation/aim-experiment-guide/) | Track and compare research experiments with Aim experiment tracker |
+| [claude-academic-workflow-guide](../../skills/research/automation/claude-academic-workflow-guide/) | Claude Code template for LaTeX, Beamer, and R research workflows |
+| [coexist-ai-guide](../../skills/research/automation/coexist-ai-guide/) | Modular MCP-based research assistant framework |
+| [data-collection-automation](../../skills/research/automation/data-collection-automation/) | Automate survey deployment, data collection, and pipeline management |
+| [datagen-research-guide](../../skills/research/automation/datagen-research-guide/) | AI-driven multi-agent research assistant for end-to-end studies |
+| [foam-agent-guide](../../skills/research/automation/foam-agent-guide/) | Agent for automated knowledge graph building from research notes |
+| [kedro-pipeline-guide](../../skills/research/automation/kedro-pipeline-guide/) | Build reproducible data science pipelines with Kedro for research projects |
+| [mle-agent-guide](../../skills/research/automation/mle-agent-guide/) | Intelligent companion for ML engineering with arXiv integration |
+| [paper-to-agent-guide](../../skills/research/automation/paper-to-agent-guide/) | Transform research papers into interactive AI agents for exploration |
+| [rd-agent-guide](../../skills/research/automation/rd-agent-guide/) | Microsoft AI-driven R&D agent for automated data and model development |
+| [research-paper-orchestrator](../../skills/research/automation/research-paper-orchestrator/) | Master orchestrator coordinating 10 specialized subagents for papers |
+| [research-workflow-automation](../../skills/research/automation/research-workflow-automation/) | Automate repetitive research tasks with pipelines, schedulers, and scripting |
+
+
+## Deep Research
+
+
+| Skill | Description |
+|-------|-------------|
+| [academic-deep-research](../../skills/research/deep-research/academic-deep-research/) | Multi-cycle exhaustive investigation framework for academic topics |
+| [auto-deep-research-guide](../../skills/research/deep-research/auto-deep-research-guide/) | Automated deep research tool for thorough topic investigation |
+| [cognitive-kernel-guide](../../skills/research/deep-research/cognitive-kernel-guide/) | Autonomous agent with long-term memory for deep research tasks |
+| [corvus-research-guide](../../skills/research/deep-research/corvus-research-guide/) | Multi-agent AI research with semantic search and citation snowballing |
+| [deep-research-pro](../../skills/research/deep-research/deep-research-pro/) | Multi-source deep research agent with verification and synthesis |
+| [deep-research-work](../../skills/research/deep-research/deep-research-work/) | Combine web search, content analysis, and source verification |
+| [deep-searcher-guide](../../skills/research/deep-research/deep-searcher-guide/) | Open deep research alternative for private data with vector search |
+| [gpt-researcher-guide](../../skills/research/deep-research/gpt-researcher-guide/) | Autonomous agent for comprehensive deep research on any topic |
+| [in-depth-research-guide](../../skills/research/deep-research/in-depth-research-guide/) | Structured methodology for conducting exhaustive multi-source investigations |
+| [khoj-research-guide](../../skills/research/deep-research/khoj-research-guide/) | AI second brain for deep research and personal knowledge management |
+| [kosmos-scientist-guide](../../skills/research/deep-research/kosmos-scientist-guide/) | Claude Code-driven autonomous AI Scientist for discovery |
+| [llm-scientific-discovery-guide](../../skills/research/deep-research/llm-scientific-discovery-guide/) | Survey of LLM agents for biomedical scientific discovery |
+| [local-deep-research-guide](../../skills/research/deep-research/local-deep-research-guide/) | Deep research agent searching 10+ sources with local or cloud LLMs |
+| [meta-synthesis-guide](../../skills/research/deep-research/meta-synthesis-guide/) | Conduct qualitative meta-synthesis and evidence synthesis methods |
+| [open-researcher-guide](../../skills/research/deep-research/open-researcher-guide/) | Open pipeline for generating deep research trajectories with LLMs |
+| [research-cog](../../skills/research/deep-research/research-cog/) | Deep research powered by CellCog for comprehensive investigations |
+| [scoping-review-guide](../../skills/research/deep-research/scoping-review-guide/) | Scoping review methodology for broad evidence mapping |
+| [systematic-review-guide](../../skills/research/deep-research/systematic-review-guide/) | Systematic review methodology with PRISMA and evidence synthesis |
+| [tongyi-deep-research-guide](../../skills/research/deep-research/tongyi-deep-research-guide/) | Open-source deep research agent by Alibaba for scholarly research |
+
+
+## Funding
+
+
+| Skill | Description |
+|-------|-------------|
+| [eu-horizon-guide](../../skills/research/funding/eu-horizon-guide/) | Navigate EU Horizon Europe funding programs and proposal writing |
+| [figshare-api](../../skills/research/funding/figshare-api/) | Research data sharing and repository |
+| [grant-budget-guide](../../skills/research/funding/grant-budget-guide/) | Prepare and justify research grant budgets across funding agencies |
+| [grant-writing-guide](../../skills/research/funding/grant-writing-guide/) | Write competitive research proposals with clear objectives and budgets |
+| [nih-reporter-api-guide](../../skills/research/funding/nih-reporter-api-guide/) | Search NIH-funded grants and research projects via RePORTER API |
+| [nsf-award-api-guide](../../skills/research/funding/nsf-award-api-guide/) | Search NSF awards and grants with free public API, no auth required |
+| [nsf-grant-guide](../../skills/research/funding/nsf-grant-guide/) | Navigate NSF grant applications, program selection, and strategies |
+| [open-science-guide](../../skills/research/funding/open-science-guide/) | Pre-registration, open data, and FAIR principles for research |
+| [zenodo-api](../../skills/research/funding/zenodo-api/) | Open research repository for all disciplines |
 
-> Hand-picked resources for academic researchers working with methodology, systematic review, automation, and funding.
 
 ## Methodology
 
-### Research Design Guides
-- **[Research Design: Qualitative, Quantitative, and Mixed Methods (Creswell)](https://us.sagepub.com/en-us/nam/research-design/book270550)** — Standard textbook on research design across paradigms; used in most graduate methods courses.
-- **[EQUATOR Network](https://www.equator-network.org/)** — Library of reporting guidelines (CONSORT, STROBE, PRISMA, etc.) for health research.
-- **[NIH Research Methods Resources](https://researchmethodsresources.nih.gov/)** — Guides on study design, sample size estimation, and statistical analysis plans from NIH.
-- **[Research Design Canvas](https://www.researchdesigncanvas.com/)** — Visual tool for mapping research questions, methods, and expected outcomes on a single page.
-
-### Design of Experiments (DOE)
-- **[JMP Statistical Discovery](https://www.jmp.com/en/statistics-knowledge-portal/design-of-experiments.html)** — Comprehensive DOE knowledge portal with interactive examples.
-- **[pyDOE2](https://github.com/clicumu/pyDOE2)** — Python library for generating factorial, Latin Hypercube, and composite experimental designs.
-- **[Design-Expert (Stat-Ease)](https://www.statease.com/software/design-expert/)** — GUI software for designing and analyzing multi-factor experiments; free trial.
-
-## Deep Research & Systematic Review
-
-### Tools & Software
-- **[Covidence](https://www.covidence.org/)** — Streamlined systematic review management: screening, extraction, quality assessment. Free for Cochrane authors.
-- **[Rayyan](https://www.rayyan.ai/)** — Free AI-assisted tool for systematic review screening; supports team collaboration.
-- **[ASReview](https://asreview.nl/)** — Open-source active-learning tool that prioritizes relevant papers during screening; dramatically reduces workload.
-- **[PRISMA 2020](http://www.prisma-statement.org/)** — Updated reporting checklist and flow diagram for systematic reviews and meta-analyses.
-- **[RevMan (Cochrane)](https://training.cochrane.org/online-learning/core-software/revman)** — Free software for preparing Cochrane systematic reviews and meta-analyses.
-
-### Key References
-- **[Cochrane Handbook for Systematic Reviews](https://training.cochrane.org/handbook)** — The definitive methodological guide for systematic reviews in health and beyond.
-- **[PROSPERO](https://www.crd.york.ac.uk/prospero/)** — International registry of systematic review protocols; register before you begin.
-
-## Paper Review & Summarization
-
-### Tools & Software
-- **[ScholarAI](https://scholarai.io/)** — AI plugin that finds, summarizes, and extracts key claims from academic papers.
-- **[Consensus](https://consensus.app/)** — AI search engine that extracts and synthesizes claims from peer-reviewed papers.
-- **[SciSpace (Typeset)](https://typeset.io/)** — AI copilot for reading papers: highlights, explains, and cross-references passages.
-- **[OpenReview](https://openreview.net/)** — Open platform for peer review used by ICLR, NeurIPS, and other top ML conferences.
-- **[Semantic Reader (S2)](https://www.semanticscholar.org/product/semantic-reader)** — AI-augmented PDF reader from Semantic Scholar with inline citation context and term definitions.
-
-## Research Automation
-
-### AI Scientist & Workflow Tools
-- **[PaperQA2](https://github.com/Future-House/paper-qa)** — RAG system that answers questions using full-text scientific papers with proper citations.
-- **[OpenScholar](https://github.com/AkariAsai/OpenScholar)** — Open-source scientific literature QA agent from University of Washington.
-- **[Snakemake](https://snakemake.readthedocs.io/)** — Reproducible and scalable workflow engine for data analysis pipelines; Python-based.
-- **[Nextflow](https://www.nextflow.io/)** — Workflow manager for computational pipelines; strong in bioinformatics and genomics.
-- **[DVC (Data Version Control)](https://dvc.org/)** — Git for data and ML experiments; tracks datasets, models, and metrics alongside code.
-- **[MLflow](https://mlflow.org/)** — Open-source platform for managing the ML lifecycle: tracking, packaging, deployment.
-
-## Funding & Open Science
-
-### Grant Databases
-- **[NIH Reporter](https://reporter.nih.gov/)** — Searchable database of NIH-funded research projects; essential for US biomedical grant intelligence.
-- **[NSF Award Search](https://www.nsf.gov/awardsearch/)** — Browse and search all NSF-funded awards; useful for understanding funding landscapes.
-- **[Dimensions Grants](https://app.dimensions.ai/discover/grant)** — Global grant database linking funders, publications, patents, and clinical trials.
-- **[Europe PMC Grant Finder](https://europepmc.org/grantfinder)** — Search grants from major European and international funders.
-
-### Open Science Platforms
-- **[OSF (Open Science Framework)](https://osf.io/)** — Free platform for project management, preregistration, preprints, and data sharing.
-- **[Zenodo](https://zenodo.org/)** — CERN-hosted open repository for datasets, software, and publications; DOI minting included.
-- **[protocols.io](https://www.protocols.io/)** — Open-access platform for sharing, discovering, and discussing research protocols.
-- **[ORCID](https://orcid.org/)** — Persistent digital identifier for researchers; connects your work across systems.
+
+| Skill | Description |
+|-------|-------------|
+| [academic-mentor-guide](../../skills/research/methodology/academic-mentor-guide/) | AI research advisor for graduate students navigating academic careers |
+| [action-research-guide](../../skills/research/methodology/action-research-guide/) | Design and conduct action research and participatory studies |
+| [claude-scientific-guide](../../skills/research/methodology/claude-scientific-guide/) | Ready-to-use agent skills for scientific research and engineering |
+| [deep-innovator-guide](../../skills/research/methodology/deep-innovator-guide/) | AI research for idea generation and scientific discovery methods |
+| [experimental-design-guide](../../skills/research/methodology/experimental-design-guide/) | Design rigorous experiments using DOE, factorial designs, and response surfaces |
+| [grad-school-guide](../../skills/research/methodology/grad-school-guide/) | Practical advice for thriving in PhD programs and academic research |
+| [grounded-theory-guide](../../skills/research/methodology/grounded-theory-guide/) | Apply grounded theory methodology to develop theory from data |
+| [mixed-methods-guide](../../skills/research/methodology/mixed-methods-guide/) | Guide to designing and conducting mixed methods research |
+| [osf-api-guide](../../skills/research/methodology/osf-api-guide/) | Access Open Science Framework for preregistrations, preprints, and data |
+| [parsifal-slr-guide](../../skills/research/methodology/parsifal-slr-guide/) | Plan and manage systematic literature reviews with Parsifal platform |
+| [qualitative-research-guide](../../skills/research/methodology/qualitative-research-guide/) | Design and conduct qualitative research using grounded theory, case studies, ... |
+| [research-paper-kb](../../skills/research/methodology/research-paper-kb/) | Build a persistent cross-session knowledge base from academic papers |
+| [research-pipeline-units-guide](../../skills/research/methodology/research-pipeline-units-guide/) | Evidence-first semantic research pipeline methodology |
+| [research-town-guide](../../skills/research/methodology/research-town-guide/) | Simulate human research communities with multi-agent AI collaboration |
+| [scientify-idea-generation](../../skills/research/methodology/scientify-idea-generation/) | Generate research ideas from collected papers with gap analysis |
+| [slr-automation-guide](../../skills/research/methodology/slr-automation-guide/) | Tools and pipelines for automating systematic literature reviews |
+
+
+## Paper Review
+
+
+| Skill | Description |
+|-------|-------------|
+| [automated-review-guide](../../skills/research/paper-review/automated-review-guide/) | AI-assisted peer review tools, workflows, and quality standards |
+| [latte-review-guide](../../skills/research/paper-review/latte-review-guide/) | Automate systematic literature reviews with LatteReview AI agents |
+| [paper-compare-guide](../../skills/research/paper-review/paper-compare-guide/) | Compare research papers side-by-side on methodology and findings |
+| [paper-critique-framework](../../skills/research/paper-review/paper-critique-framework/) | Structured framework for writing peer review reports and paper critiques |
+| [paper-digest-guide](../../skills/research/paper-review/paper-digest-guide/) | Fetch paper and spawn sub-agents to read citations recursively |
+| [paper-reading-assistant](../../skills/research/paper-review/paper-reading-assistant/) | AI-assisted paper reading, PDF Q&A, and summarization workflows |
+| [paper-research-assistant](../../skills/research/paper-review/paper-research-assistant/) | Read papers, generate structured reports, find code and datasets |
+| [peer-review-guide](../../skills/research/paper-review/peer-review-guide/) | Conduct thorough, constructive peer reviews and evaluate research papers crit... |
+| [rebuttal-writing-guide](../../skills/research/paper-review/rebuttal-writing-guide/) | Write effective rebuttals to reviewer comments for journal submissions |
+| [research-quality-filter](../../skills/research/paper-review/research-quality-filter/) | Filter and assess research paper quality using structured criteria |
+| [review-response-guide](../../skills/research/paper-review/review-response-guide/) | Craft effective point-by-point reviewer response letters |
+| [scientify-write-review-paper](../../skills/research/paper-review/scientify-write-review-paper/) | Write literature reviews and survey papers from collected papers |