「pathways」の検索結果

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".

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WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.

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Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run enrichGO/enrichKEGG/enrichPathway/enrichWP or gseGO/gseKEGG (clusterProfiler, ReactomePA, rWikiPathways), and visualize. Use when a DESeq2/edgeR/limma result must become enriched GO terms, KEGG/Reactome/WikiPathways pathways, or a GSEA leading edge; when the input is a full ranking for all genes (GSEA, named decreasing vector) or only a pre-selected list (ORA plus a defensible background universe); or when assembling DE-to-pathway end to end. The DE list and ranking statistic come from differential-expression/de-results; per-method nuance lives in the pathway-analysis skills.

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Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Triggers on "kegg", "pathway", "metabolic pathway", "signaling pathway", "pathway genes".

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KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.

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Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.

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This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.

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GitHub 解封 — 账号封禁/限制/恢复的领域操作系统。覆盖：(a) GitHub 官方政策体系 (TOS / 可接受使用政策 / Trust & Safety 执行模式 / 公开申诉路径 / 受制裁地区解读)；(b) 封号原因诊断学 (spam / abuse / 制裁误标 / 2FA 丢失 / ToS 违规 / 账号劫持误判 / ban evasion 等子类型 + 症状→原因映射 + 自我分诊压测)；(c) 申诉实操 craft (写一封能让 T&S 快速判误伤的英文申诉信 + 升级阶梯 + 法务介入边界 + Don'ts)；(d) 制裁与合规硬边界 (OFAC SDN 名单 / 哪些国家或地区真不可达 / VPN 误判路径 / 中国大陆不是美国制裁地区的反复重申)；(e) 中国大陆开发者特别处境 (sanctioned region 误标 + SMS 验证不支持 +86/+852 + Gitee/GitLab/Codeberg/JihuLab 备用迁移 + 私有自托管 Gitea/Forgejo)；(f) 真实案例库 (~30+ 公开案例分类拆解：误伤 / 真违规 / 制裁误标三类各自赔率与申诉成功路径)。伦理锚绝不软化：不教 ban evasion / 不教撒谎式申诉 / 真违规承认改进 / 丢 2FA 无恢复因子则诚实告知 / 中国制裁误标靠申诉不靠换 VPN / 申诉 6 个月窗口必算清 / 约 3% (业内估) 真违规恢复 vs 约 79% (业内估) 误伤申诉成功率分层标。 (GitHub Account Reinstatement — the domain operating system for GitHub (and analogous platform) account suspension, restriction, appeal, and recovery. Covers: (a) GitHub official policy architecture (TOS / Acceptable Use Policies / Trust & Safety enforcement patterns / public appeals pathways / sanctioned-region interpretation); (b) suspension-cause diagnostics (spam / abuse / sanctions mis-flag / 2FA loss / ToS violation / account hijack false-positive / ban evasion taxonomy + symptom→cause mapping + self-triage pressure test); (c) appeal craft (writing an English appeal letter that gets T&S to fast-track a false-positive ruling + escalation ladder + legal-engagement boundary + Don'ts); (d) sanctions and compliance hard boundaries (OFAC SDN list / which countries/regions are truly unreachable / VPN false-positive paths / China is NOT a US-sanctioned region — repeated emphasis); (e) mainland China developer special circumstances (sanctioned-region mis-flag + SMS verification does not support +86/+852 + Gitee/GitLab/Codeberg/JihuLab fallback migration + self-hosted Gitea/Forgejo); (f) real-case library (~30+ public cases with categorized analysis: false-positive / genuine violation / sanctions mis-flag, each with win-rate and appeal success path). Ethical anchors absolutely not softened: do NOT teach ban evasion (creating new accounts turns a temp ban into a permanent one — the single biggest mistake); do NOT teach social engineering or lying in appeals (misuse + actually confirms violation); genuine violations: admit + improve beats denial; lost 2FA + no recovery factor → do not pretend recovery is possible; China sanctioned-region mis-flag → fix via appeal, not repeated VPN switching; appeal form 6-month window must be counted carefully; historical 约 3% (业内估) genuine-violation recovery vs 约 79% (业内估) false-positive appeal success rate stratification must be honestly labeled. Anti-samples (explicitly describe harm, never endorse): developer permabanned for ban evasion / open-source team org-banned for personal attacks in public issues / cases where repeated VPN switching escalated risk-control severity.) Master OS — automated mastery of GitHub Account Reinstatement — the domain operating system for GitHub (and analogous platform) account suspension, restriction, appeal, and recovery. Covers: (a) GitHub official policy architecture (TOS / Acceptable Use Policies / Trust & Safety enforcement patterns / public appeals pathways / sanctioned-region interpretation); (b) suspension-cause diagnostics (spam / abuse / sanctions mis-flag / 2FA loss / ToS violation / account hijack false-positive / ban evasion taxonomy + symptom→cause mapping + self-triage pressure test); (c) appeal craft (writing an English appeal letter that gets T&S to fast-track a false-positive ruling + escalation ladder + legal-engagement boundary + Don'ts); (d) sanctions and compliance hard boundaries (OFAC SDN list / which countries/regions are truly unreachable / VPN false-positive paths / China is NOT a US-sanctioned region — repeated emphasis); (e) mainland China developer special circumstances (sanctioned-region mis-flag + SMS verification does not support +86/+852 + Gitee/GitLab/Codeberg/JihuLab fallback migration + self-hosted Gitea/Forgejo); (f) real-case library (~30+ public cases with categorized analysis: fa

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Expert-level biochemistry from a biology perspective covering metabolic pathways, enzyme kinetics, bioenergetics, signal transduction, and the biochemical basis of cellular processes.

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METAINFORMANT rules for directory src/metainformant/multiomics/pathways. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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METAINFORMANT rules for directory src/metainformant/metabolomics/pathways. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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KEGG-based disease-drug-variant network research. Connects diseases to causal genes, drugs to molecular targets, and variants to pathways using KEGG's editorially curated databases (KEGG Disease, Drug, Network, Variant, Pathway). Use for drug repurposing via shared pathways, mechanistic disease-gene-drug networks, and pathway-based target discovery. Distinguishes direct (binding) vs indirect (pathway co-membership) drug-target relationships.

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Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mummichog/PSEA on raw m/z peaks, and network-diffusion enrichment (FELLA), with correct background-set construction and honest interpretive ceilings. Use when interpreting differential metabolites or an untargeted LC-MS feature table in pathway context, choosing ORA vs MSEA vs mummichog vs topology, or setting the reference/background set. For annotation confidence levels feeding ORA see metabolomics/metabolite-annotation; for gene-set concepts see pathway-analysis/go-enrichment and pathway-analysis/gsea; for joint gene+metabolite pathways see multi-omics-integration/mofa-integration.

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Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.7 Flash for quality review. Refines when the review requests improvement, with at most two generations. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

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Generates or edits images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrations, artwork, concept art, visual assets, logos, and image editing or compositing from reference images. For flowcharts, circuits, pathways, and other technical diagrams, use the scientific-schematics skill instead.

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Senior Regulatory Affairs Manager for HealthTech and MedTech companies. Prepares FDA 510(k), De Novo, and PMA submission packages; analyzes regulatory pathways for new medical devices; drafts responses to FDA deficiency letters and Notified Body queries; develops CE marking technical documentation under EU MDR 2017/745; coordinates multi-market approval strategies across FDA, EU, Health Canada, PMDA, and NMPA; and maintains regulatory intelligence on evolving standards. Use when users need to plan or execute FDA submissions, navigate 510(k) or PMA approval processes, achieve CE marking, prepare pre-submission meeting materials, write regulatory strategy documents, respond to agency queries, or manage compliance documentation for medical device market access.

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Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries

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Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

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Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

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Comprehensive markdown and Mermaid diagram writing skill that establishes text-based diagrams as the DEFAULT documentation standard. Use this skill when creating ANY scientific document, report, analysis, or visualization — it ensures all outputs are in version-controlled, token-efficient markdown with embedded Mermaid diagrams as the source of truth, with clear pathways to downstream Python or AI-generated images. Includes full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates ready to use.

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Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.

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Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.

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Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classes, chain composition, or lipid-specific pathways.

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Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.

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