「papers」の検索結果

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.

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Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with CVD-safe palettes, cairo_pdf TrueType embedding, programmatic aes via tidy evaluation, and the theme_classic publication baseline. Use when producing static figures in R for papers, presentations, or reports.

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Use this skill when the user asks about hazardous materials (hazmat) transportation under 49 CFR 171-180 — placarding requirements, segregation tables, hazmat employee training (49 CFR 172 Subpart H), Hazmat Safety Permit (HMSP), shipping papers, packaging groups, emergency response phone, security plans, hazmat endorsement on CDL, and bulk vs non-bulk distinctions. Cite specific 49 CFR section.

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Comprehensive toolkit for writing high-quality computer science research papers (conference, journal, thesis). Provides narrative construction guidance, sentence-level clarity principles (Gopen & Swan), academic phrasebank, CS-specific conventions, and section-by-section quality checklists. Use when assisting with academic paper writing, revision, or structure planning across all stages from drafting to submission.

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Expert guidance for reviewing academic manuscripts submitted to journals, particularly in political science, economics, and quantitative social sciences. Use when asked to review, critique, or provide feedback on academic papers, research designs, or empirical strategies. Emphasizes methodological rigor, causal identification strategies, and constructive feedback on research design.

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Interactive review sessions with academic PDFs (lectures, research papers, book chapters). Extract concepts, run Q&A sessions, generate quizzes with scoring. Preserves mathematical formulas in LaTeX format. Privacy-preserving local processing - PDFs never uploaded. Use when studying academic materials, reviewing research, or preparing for exams.

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Use when writing CS research papers (conference, journal, thesis), reviewing scientific manuscripts, improving academic writing clarity, or preparing IEEE/ACM submissions. Invoke when user mentions paper, manuscript, research writing, journal submission, or needs help with academic structure, formatting, or revision.

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End-to-end pipeline for writing ML/AI research papers — from experiment design through analysis, drafting, revision, and submission. Covers NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Integrates automated experiment monitoring, statistical analysis, iterative writing, and citation verification.

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Search and retrieve academic papers from arXiv using their free REST API. No API key needed. Search by keyword, author, category, or ID. Combine with web_extract or the ocr-and-documents skill to read full paper content.

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Use this skill when the user requests to review, analyze, critique, or summarize academic papers, research articles, preprints, or scientific publications. Supports comprehensive structured reviews covering methodology assessment, contribution evaluation, literature positioning, and constructive feedback generation. Trigger on queries involving paper URLs, uploaded PDFs, arXiv links, or requests like "review this paper", "analyze this research", "summarize this study", or "write a peer review".

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Research synthesis from sources — "summarize these URLs or papers", "research this topic with these sources", "create a podcast about", "audio overview", "mind map", "quiz from these sources", "flashcards", "deep research on". Wraps Google NotebookLM via notebooklm-py.

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Write long-form and channel content — articles, blog posts, documentation, newsletters, whitepapers, books, copywriting. The CMO office's primary execution skill for anything written.

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Process and manipulate images using ImageMagick. Supports resizing, format conversion, batch processing, and retrieving image metadata. Use when working with images, creating thumbnails, resizing wallpapers, or performing batch image operations.

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Add real references and standardize citations for research papers and theses (为科研论文和毕业论文添加真实参考文献并规范引用标注)

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Write ML papers for NeurIPS/ICML/ICLR: design→submit.

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Creates professional PDF whitepapers from Markdown files. Use when the user wants to create a whitepaper, technical document, or PDF with professional formatting and typography.

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Use for any question about a codebase, its architecture, file relationships, or project content — especially when graphify-out/ exists, where the question should be treated as a graphify query first. Turns any input (code, docs, papers, images, videos) into a persistent knowledge graph with god nodes, community detection, and query/path/explain tools.

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Neural web search and code context via Exa AI API. Requires EXA_API_KEY. Use for finding documentation, code examples, research papers, or company info.

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Generate professional PDFs from Markdown using Pandoc and LaTeX with AI-powered content generation. Creates whitepapers, term sheets, memos, agreements, SAFEs, NDAs, and more.

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Generates full long-form content: whitepapers, eBooks, research reports, and pillar pages. Takes a content brief and produces 2000-5000 word drafts with sections, data points, and CTAs.

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Defensive counterpart to federated-harbor-redteam: closes the smells that red team opens against The Federated Harbor whitepaper. Federation-specific defenses for cross-harbor primitives — mechanization commitments, scope hedges, cross-paper dependency formalization, pre-emptive analogies (CT, Macaroons, atomic swaps), and defense-in-depth framing (refuses vs prices). Use during a versioned red-vs-white round; pairs with federated-harbor-redteam. NOT for ad-hoc code review, NOT for the Anchor or Bonded papers (use whitehat-defense).

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Adversarial reviewer for The Federated Harbor whitepaper — the third paper in the Curiositech sequence after Anchor and Bonded Commons. Probes federation-specific threats: trust transitivity, cross-harbor token forgery, federated revocation under partition, cross-harbor Sybil, cross-domain settlement, equivocation, bond-pool draining, cold-start joining, federation-operator Sybil. Use during a versioned red-vs-white round; pairs with federated-harbor-whitehat. NOT for incident response, NOT for the Anchor or Bonded papers (use redteam-review).

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Drafting and iterating sections of The Federated Harbor whitepaper — the third paper in the Curiositech sequence after Anchor (local identity) and Bonded Commons (local coordination), extending coordination across machines and administrative domains. Use when authoring a section, rewriting a section after a redteam/whitehat round, or composing a new chapter. NOT for marketing copy, NOT for the other two papers, NOT for production threat response.

日本語の概要は準備中です。原文の説明を表示しています。