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Research

Scientific computing and academic tools.

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computational-chemistry
1

whitepaper-editor

Brutal technical white paper editor that performs merciless review with research-backed validation. Use when reviewing, editing, or improving white papers, technical documents, research papers, or any document requiring rigorous technical scrutiny. Triggers on requests to review white papers, validate citations, check technical accuracy, perform gap analysis, or score document quality.

NimbleBrainInc
NimbleBrainInc
research
open
academic
1

arxiv-doc-builder

Automatically convert arXiv papers to well-structured Markdown documentation. Invoke with an arXiv ID to fetch materials (LaTeX source or PDF), convert to Markdown, and generate implementation-ready reference documentation with preserved mathematics and section structure.

ultimatile
ultimatile
research
open
academic
1

pdf-tools

Search and extract content from PDF files. Use when searching PDFs, finding text in documents, or extracting specific pages without reading the entire file.

caiopizzol
caiopizzol
research
open
academic
1

zotero-paper-reader

Read and analyze academic papers from Zotero library. Use when the user requests to read, access, or analyze a paper by title, author, or topic from their Zotero library. Automatically searches Zotero, converts PDFs to markdown, saves to Notes/PaperInMarkdown, and provides analysis.

FuZhiyu
FuZhiyu
research
open
scientific-computing
1

expert-analysis

Deep analysis of documentation/articles with practical application guidance. Use when user asks to "analyze and apply", "digest and implement", "read and integrate", or provides a document they want analyzed for implementation in the codebase.

NicktheQuickFTW
NicktheQuickFTW
research
open
scientific-computing
1

pydeseq2

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

hxk622
hxk622
research
open
scientific-computing
1

hypogenic

Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.

hxk622
hxk622
research
open
scientific-computing
1

deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

hxk622
hxk622
research
open
bioinformatics
1

networkx

Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.

hxk622
hxk622
research
open
scientific-computing
1

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

hxk622
hxk622
research
open
scientific-computing
1

design-synthesis

Synthesizes research findings into design decisions via codebase investigation. Use when (1) translating research into implementation approaches, (2) selecting between design alternatives, (3) executing after /research or deep-research, or (4) preparing input for /plan phase.

bsamiee
bsamiee
research
open
academic
1

researcher-report-templates

Generate structured research reports with findings, comparisons, recommendations, and citations. Use when documenting investigation results or creating technical comparisons. This skill provides comprehensive research report templates: - Investigation findings with proper structure - Technology comparison tables - Best practices summaries - Citation and reference management - Executive summaries Triggers: "create report", "summarize findings", "compare technologies", "research report", "調査レポート", "技術比較", "ベストプラクティス"

takemi-ohama
takemi-ohama
research
open
academic
1

academic-researcher

Extracts structured data from cybersecurity fatigue research papers and calculates statistical correlations

Tristan578
Tristan578
research
open
scientific-computing
1

reactome-database

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

hxk622
hxk622
research
open
academic
1

data-fetch

Fetch and aggregate data from 17 external APIs including Census, arXiv, NASA, Wikipedia, PubMed, and GitHub.

lukeslp
lukeslp
research
open
scientific-computing
1

airalogy-protocol

Expert guide for creating Airalogy Protocols (AIMD), Assigners (Python logic), and Validation Models. Use this to design digital workflows and experiments.

airalogy
airalogy
research
open
academic
1

summarize-robotics-text

Summarize robotics-related text, research papers, or lecture notes into concise, clear, and structured summaries. Use when user asks to condense or simplify robotics content.

MuhammadHassaanArain
MuhammadHassaanArain
research
open
computational-chemistry
1

mechinterp-glossary-and-constraints

Reference skill for Splatoon ability families, AP rungs, token constraints, and domain rules for mechinterp experiments

cesaregarza
cesaregarza
research
open
academic
1

learning-graph-generator

Generates a comprehensive learning graph from a course description, including 200 concepts with dependencies, taxonomy categorization, and quality validation reports. Use this when the user wants to create a structured knowledge graph for educational content.

dmccreary
dmccreary
research
open
academic
1

gpt-researcher

Run GPT-Researcher multi-agent deep research framework locally using OpenAI GPT-5.2. Replaces ChatGPT Deep Research with local control. Researches 100+ sources in parallel, provides comprehensive citations. Use for Phase 3 industry/technical research or comprehensive synthesis. Takes 6-20 min depending on report type. Supports multiple LLM providers.

yudame
yudame
research
open
academic
1

llm-optimization

Optimize websites for AI assistant recommendations. ChatGPT, Gemini, Perplexity, Claude. Get cited in AI answers.

Soborbo
Soborbo
research
open
academic
1

layer-definitions

Provide L1-L5 pedagogy layer reference for the AI-Native Robotics Textbook. Use when assigning layers to content, understanding layer requirements, or validating layer progression.

zeeshan080
zeeshan080
research
open
academic
1

research-and-fact-checker

Performs accurate research and fact-checking using reliable sources. Ideal for validating claims, clarifying complex topics, summarizing findings, and ensuring information accuracy.

codeWithHak
codeWithHak
research
open
academic
1

firecrawl

Web scraping, content extraction, and autonomous research agent for deep web investigation.

5dlabs
5dlabs
research
open
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