Browse Skills — Page 108

enhance-prompt

diegosouzapw/awesome-omni-skills

Enhance Prompt for Stitch workflow skill. Use this skill when the user needs Transforms vague UI ideas into polished, Stitch-optimized prompts. Enhances specificity, adds UI/UX keywords, injects design system context, and structures output for better generation results and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

enhance-prompt

google-labs-code/stitch-skills

Transforms vague UI ideas into polished, Stitch-optimized prompts. Enhances specificity, adds UI/UX keywords, injects design system context, and structures output for better generation results.

enhance-prompt-v2

diegosouzapw/awesome-omni-skills

Enhance Prompt for Stitch workflow skill. Use this skill when the user needs Transforms vague UI ideas into polished, Stitch-optimized prompts. Enhances specificity, adds UI/UX keywords, injects design system context, and structures output for better generation results and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

enhanced-volcano-plot

swaruplab/operon

Publication-quality volcano plots from DE results using EnhancedVolcano (R) or matplotlib (Python).

enigma-automation

ComposioHQ/awesome-claude-skills

"Automate Enigma tasks via Rube MCP (Composio). Always search tools first for current schemas."

enrich-company-and-contact-data

openai/role-specific-plugins

Use for data-first company, contact, lead, and prospect discovery or enrichment, including firmographic or technographic completion, named-company profiling, entity resolution, ICP matching, prospect-list building, segmentation, trigger or sales-signal analysis, market and territory scans, and enrichment-backed comparisons. Exclude meeting preparation, outreach-led company research, and prioritization of an already established account book.

enrich-ioc

dandye/ai-runbooks

"Enrich an IOC (IP, domain, hash, URL) with threat intelligence. Use when you need to look up reputation and context for an indicator using GTI and SIEM. Returns threat intel findings, SIEM entity summary, and IOC match status."

enrich-lead

anthropics/knowledge-work-plugins

"Instant lead enrichment. Drop a name, company, LinkedIn URL, or email and get the full contact card with email, phone, title, company intel, and next actions."

enrich-paper

huggingface/paperswithcode

>-

enrichment-design

extruct-ai/gtm-skills

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ens-primary-name

BankrBot/skills

Set your primary ENS name on Base and other L2s. Use when user wants to set their ENS name, configure reverse resolution, set primary name, or make their address resolve to an ENS name. Supports Base, Arbitrum, Optimism, and Ethereum mainnet.

ensembl-database

jaechang-hits/SciAgent-Skills

Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.

ensembl-sequence-retrieval

InternScience/scp

Retrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.

ensembl-skill

openai/plugins

Submit compact Ensembl REST API requests for lookup, overlap, cross-reference, and variation endpoints. Use when a user wants concise Ensembl summaries

ensemble-solving

mhattingpete/claude-skills-marketplace

Generate multiple diverse solutions in parallel and select the best. Use for architecture decisions, code generation with multiple valid approaches, or creative tasks where exploring alternatives improves quality.

ensure-docs

existential-birds/beagle

Verify documentation coverage and generate missing docs interactively

ensure-pipelines-host

microsoft/power-platform-skills

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ensure-test-coverage

UKGovernmentBEIS/inspect_evals

Ensure test coverage for a single evaluation - both reviewing existing tests and creating missing ones. Analyzes testable components, checks tests against repository conventions, reports coverage gaps, and creates or improves tests. Use when user asks to check/review/create/add/ensure tests for an eval. Use whenever you are asked to review an evaluation that contains tests, or whenever you need to write a suite of tests. Do NOT use for fixing a specific failing CI test (use ci-maintenance-workflow instead).

entelligence-automation

ComposioHQ/awesome-claude-skills

"Automate Entelligence tasks via Rube MCP (Composio). Always search tools first for current schemas."

enter-services

pollinations/pollinations

Deploy and manage enter.pollinations.ai text/image services on EC2 and Cloudflare Workers. Requires: SSH keys, sops, wrangler.

enterprise

bergside/awesome-design-skills

Dark-themed cloud-platform aesthetic with modular grids, glass-like panels, and strong data hierarchy for productivity dashboards.

enterprise-agent-ops

affaan-m/ECC

Operate long-lived agent workloads with observability, security boundaries, and lifecycle management.

enterprise-artifact-search

elizaOS/eliza

Multi-hop evidence search + structured extraction over enterprise artifact datasets (docs/chats/meetings/PRs/URLs). Strong disambiguation to prevent cross-product leakage; returns JSON-ready entities plus evidence pointers.

enterprise-deal-desk-close-plans

Significant-Gravitas/skills-catalog

Use when a large deal needs procurement, legal, security, and pricing orchestration: mutual close plans, deal-desk runs, and signature.

enterprise-identity-sso-support

Significant-Gravitas/skills-catalog

Use when logins fail at the identity layer — SAML, SSO, SCIM, OIDC, or API auth: triage the handshake, find the break, and verify every AI-drafted word before it ships.

enterprise-risk-aggregator

datadrivenconstruction/DDC_Skills_for_AI_Agents_in_Construction

Aggregate and analyze risks across construction project portfolio. Identify correlated risks, systemic exposures, and portfolio-level risk mitigation strategies.

enterprise-sales

liqiongyu/lenny_skills_plus

Create an Enterprise Deal Execution Pack (buying committee map, mutual action plan, ROI model).

enterprise-search

notque/vexjoy-agent

Enterprise search engineering — relevance tuning, query understanding, index management, search quality measurement, ranking optimization, schema design. Use when building search features, debugging relevance, tuning ranking, designing indices, or measuring search quality.

enterprise-search

anthropics/claude-tag-plugins

Search the company's enterprise knowledge index. Use this FIRST when starting any task that touches company-specific context - projects, people, policies, internal docs, prior decisions - before searching individual sources like Drive, Slack, or Jira directly. Also use it when the user asks "do we have a doc about X", "what's our policy on Y", or references internal initiatives by name. Always start from this skill when interacting with this service — its bundled scripts and recipes are the fastest path.

entfristung-elektronische-signatur-vorsicht

Klotzkette/claude-fuer-deutsches-recht

Elektronische Signaturen und Befristungsabreden: qualifizierte elektronische Signatur genuegt NICHT fuer § 14 Abs. 4 TzBfG i.V.m. § 126 BGB; DocuSign Adobe Sign HelloSign als Erkennungsmerkmale; Unterscheidung einfache fortgeschrittene qualifizierte elektronische Signatur; Rechtsfolge § 16 Satz 1 TzBfG unbefristeter Vertrag.

entfristung-grundwarnung-drei-wochen-frist

Klotzkette/claude-fuer-deutsches-recht

Grundwarnung Entfristungsklage: § 17 TzBfG drei Wochen ab vereinbartem Vertragsende; absolute Ausschlussfrist; § 17 Satz 2 TzBfG i.V.m. § 7 KSchG Fiktion Wirksamkeit der Befristung bei Fristversaeumnis; Fristberechnung; nachtraegliche Zulassung.

entfristung-guetetermin-und-kammertermin-sprechzettel

Klotzkette/claude-fuer-deutsches-recht

Sprechzettel fuer Guetetermin und Kammertermin in der Entfristungsklage: Antragsstellung; Kernargumente Schriftformmangel und Sachgrundmangel; Vergleichsstrategie; Vorbereitung Zeugenvernehmung; Verhandlungsposition; Normen § 54 und § 57 ArbGG.

entfristung-klageschrift-anwalt-baustein

Klotzkette/claude-fuer-deutsches-recht

Anwaltliche Klageschrift Entfristungsklage mit Hauptantrag und Hilfsantraegen; Weiterbeschaeftigungsantrag; strukturierte Begruendung nach § 14 Abs. 4 TzBfG und Sachgrundpruefung; Beweisangebote im BAG-Zitierstil.

entfristung-klageschrift-laie-baustein

Klotzkette/claude-fuer-deutsches-recht

Schritt-fuer-Schritt Klageschrift Entfristungsklage fuer Laien: Rubrum; Feststellungsantrag Unbefristetheit; Begruendungsbausteine fuer Schriftformmangel und fehlenden Sachgrund; Beweisangebote; Pflicht-Disclaimer.

entfristung-laie-oder-anwalt-frage

Klotzkette/claude-fuer-deutsches-recht

Statusabfrage Entfristungsklage: Anwalt oder Laie; bei Laie Warnungen und Empfehlung anwaltlicher Beratung; kein Mandatsverhaeltnis; Hinweis auf § 17 TzBfG Drei-Wochen-Frist als kritischste Ausschlussfrist.

entfristung-output-warnschriftsatz-laie

Klotzkette/claude-fuer-deutsches-recht

Vollstaendige Klageschrift Entfristungsklage mit Pflicht-Disclaimer fuer Laien; Zusammenfuehrung aller Bausteine; Ausfuellanleitung; Einreichungshinweise; Dreiwochenfrist-Warnblock prominent am Anfang.

entfristung-rechtsfolge-16-tzbfg-unbefristet

Klotzkette/claude-fuer-deutsches-recht

Rechtsfolge unwirksamer Befristung nach § 16 Satz 1 TzBfG: Vertrag gilt als auf unbestimmte Zeit geschlossen; Moeglichkeit der fruehesten ordentlichen Kuendigung zum vereinbarten Ende nach § 16 Satz 2 TzBfG; Ansprueche Annahmeverzug; Weiterbeschaeftigungsantrag.

entfristung-sachgrund-pruefen-14-abs-1

Klotzkette/claude-fuer-deutsches-recht

Sachgrundpruefung Befristung nach § 14 Abs. 1 TzBfG: acht Sachgruende; voruebergehender Bedarf; Vertretung; Erprobung; Eigenart der Leistung; haushaltsmittelbedingte Gruende; gerichtlicher Vergleich; BAG-Rechtsprechung zu Darlegungs- und Beweislast.

entfristung-sachgrundlos-14-abs-2-vorbeschaeftigung

Klotzkette/claude-fuer-deutsches-recht

Sachgrundlose Befristung nach § 14 Abs. 2 TzBfG: zwei Jahre Gesamtdauer; dreimal verlaengerbar; Vorbeschaeftigungsverbot; BVerfG-Entscheidung 2018; BAG-Folgerechtsprechung; Karenzzeit-Diskussion; Rechtsfolge § 16 TzBfG.

entfristung-sachgrundlos-14-abs-2a-neugruendung

Klotzkette/claude-fuer-deutsches-recht

Sachgrundlose Befristung bei Unternehmensneugründung nach § 14 Abs. 2a TzBfG: vier Jahre Gesamtdauer; Neugründungsprivileg; Voraussetzungen der Neugründung; Abgrenzung zu blossen Unternehmensumstrukturierungen.

entfristung-sachgrundlos-14-abs-3-aelter-52

Klotzkette/claude-fuer-deutsches-recht

Sachgrundlose Befristung fuer aeltere Arbeitnehmer nach § 14 Abs. 3 TzBfG: Befristung ab 52 Jahren; Voraussetzung Vorarbeitslosigkeit oder Massnahme aktiver Arbeitsmarktpolitik; EuGH-Entscheidung zur Vereinbarkeit mit Unionsrecht.

entfristung-schriftform-14-abs-4-erkennen

Klotzkette/claude-fuer-deutsches-recht

KERNSKILL: Schriftform nach § 14 Abs. 4 TzBfG fuer Befristungsabreden; eigenthaendige Unterschrift nach § 126 BGB erforderlich; KEINE elektronische Form bei Befristungsabrede; Rechtsfolge § 16 Satz 1 TzBfG Vertrag gilt als unbefristet; Vertrag selbst wirksam.

entfristung-triage-was-will-user

Klotzkette/claude-fuer-deutsches-recht

Einstieg Entfristungsklage-Workflow: Erkennung ob Nutzer Befristungskontrollklage oder Entfristungsklage anstrebt; Abgrenzung zu Kuendigungsschutzklage; Ueberblick Pruefprogramm TzBfG; Weiterleitung zu passenden Folge-Skills.

entfristung-vergleichsverhandlung-checkliste

Klotzkette/claude-fuer-deutsches-recht

Typische Vergleichsbausteine in der Entfristungsklage: Entfristungsbestaetigung oder Beendigungsdatum mit Abfindung; Weiterbeschaeftigung oder Aufhebung; Zeugnis; Freistellung; Urlaubsabgeltung; Klageerledigung; Erledigungsklausel-Risiken.

entity-audit

indranilbanerjee/digital-marketing-pro

Audit brand entity consistency. Use when: checking Wikidata, Knowledge Panel, or directory discrepancies.

entity-compliance

anthropics/claude-for-legal

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entity-model-auditor

hylarucoder/hai-stack

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entity-registry

aaron-he-zhu/aaron-marketing-skills

Use when the user asks to "optimize entity presence", reconcile an entity identity, or update canonical Knowledge Graph facts; audits and maintains machine-facing identity, sameAs, schema, disambiguation, and AI-recognition evidence through the entities registry. Not for page-level AI-citation readiness - use geo-content-optimizer; not for human-facing brand canon - use narrative-registry. 实体注册/知识图谱

entity-seo

kostja94/marketing-skills

When the user wants to optimize for entity recognition, Knowledge Graph, or entity-based SEO. Also use when the user mentions "entity SEO," "entity optimization," "Knowledge Graph," "Knowledge Panel," "entity signals," "brand entity," "entity linking," "entity relationships," or "entity-first content." For structured data, use schema-markup.

entity-seo-playbook

guia-matthieu/clawfu-skills

Use when optimizing for AI search visibility where individual experts and entities outperform generic brand pages. Use when building cross-platform authority for people, organizations, or products that AI models should recognize and cite.

entra-agent-id

microsoft/skills

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entra-agent-user

github/awesome-copilot

'Create Agent Users in Microsoft Entra ID from Agent Identities, enabling AI agents to act as digital workers with user identity capabilities in Microsoft 365 and Azure environments.'

entra-app-registration

microsoft/skills

Guides Microsoft Entra ID app registration, OAuth 2.0 authentication, and MSAL integration. USE FOR: create app registration, register Azure AD app, configure OAuth, set up authentication, add API permissions, generate service principal, MSAL example, console app auth, Entra ID setup, Azure AD authentication. DO NOT USE FOR: Key Vault secrets (use azure-keyvault-expiration-audit), general Azure resource security guidance.

entrepreneurship-and-innovation

Tibsfox/gsd-skill-creator

Entrepreneurship, innovation, and disruption for starting, scaling, and defending new ventures. Covers opportunity recognition, jobs-to-be-done, the disruptive innovation framework, sustaining vs disruptive innovation, platform businesses, network effects, minimum viable product, customer development, and the startup lifecycle from idea to exit. Use when evaluating a venture idea, positioning a new product, interpreting a competitive threat, or designing a platform.

entropy-manager

aAAaqwq/AGI-Super-Team

Entropy scanner for codebases — detect disorder and suggest cleanup actions

entry-point-analyzer

trailofbits/skills

Analyzes smart contract codebases to identify state-changing entry points for security auditing. Detects externally callable functions that modify state, categorizes them by access level (public, admin, role-restricted, contract-only), and generates structured audit reports. Excludes view/pure/read-only functions. Use when auditing smart contracts (Solidity, Vyper, Solana/Rust, Move, TON, CosmWasm) or when asked to find entry points, audit flows, external functions, access control patterns, or privileged operations.

entscheidungsbaum-ki-vo-gesamt-workflow

Klotzkette/claude-fuer-deutsches-recht

Master-Workflow: Sequenzieller Entscheidungsbaum durch die gesamte KI-VO-Pruefung. Zehn Schlusselfragen in Reihenfolge mit klaren Verzweigungen Wenn-Antwort-A-gehe-zu-Skill-X. Startpunkt des gesamten KI-VO-Pruefers fuer strukturierte Vollpruefung.

entscheidungsgruende-zivil-schreiben

Klotzkette/claude-fuer-deutsches-recht

Schreibt die Entscheidungsgruende eines Zivilurteils nach Urteilsstil (kein Gutachtenstil): Obersatz Anspruchsgrundlage Subsumtion Schluss. Reihenfolge Zulaessigkeit Begruendetheit Anspruchsgrundlage Tatbestandsmerkmale Rechtsfolge Einwendungen Einreden Verjaehrung Beweiswuerdigung Nebenentscheidungen. Verzicht auf Anspruchskonkurrenzen wenn ueberfluessig.

entwurf

Klotzkette/claude-fuer-deutsches-recht

Erstellt einen Erstentwurf häufiger Schriftstücke der Rechtsberatungsstelle — Rechtsgebiet-spezifische Muster (Widerspruchsschreiben, Mietrechtsbriefe, Klageschriften im Beratungshilfe-Kontext, Mahnschreiben), § 6 RDG-konforme Formulierung, ausdrücklich als Ausgangspunkt mit anschließender Studierenden- Analyse und Supervisoren-Freigabe. Lädt, wenn ein Studierender einen ersten Entwurf eines Schriftsatzes, Briefes, Antrags oder sonstigen Schriftstücks der Klinik benötigt.

enumeration-synthesis

yogsoth-ai/de-anthropocentric-research-engine

Synthesize all systematic enumeration outputs into a structured idea report with prioritized recommendations.

env-manager

laolaoshiren/claude-code-skills-zh

环境变量管理器：扫描、校验、同步 .env 文件，生成安全配置模板

env-secrets-manager

alirezarezvani/claude-skills

Use when auditing .env files, planning credential rotation, chasing a missing env var in production or hardening a repo against leaked secrets. Scans for committed secrets and drift with env_auditor.py.

env-setup

Tibsfox/gsd-skill-creator

Environment configuration and secrets management. Use when setting up .env files, managing secrets, or configuring environments.

env-setup-wizard

OneWave-AI/claude-skills

Set up environment variables, .env files, and configuration management. Use when configuring environment variables, creating .env files, or managing app configuration.

env-vars

openai/plugins

Vercel environment variable expert guidance. Use when working with .env files, vercel env commands, OIDC tokens, or managing environment-specific configuration.

environment-artist

arjun988/blender-skills

AAA environment art for modular kits, buildings, terrain, vegetation, architecture, and scene composition. Use for game-optimized environments, storytelling through space, and modular asset pipelines in Blender via MCP.

environment-setup-guide

benjaminasterA/antigravity-awesome-skills

Guide developers through setting up development environments with proper tools, dependencies, and configurations

environment-setup-guide-v2

diegosouzapw/awesome-omni-skills

Environment Setup Guide workflow skill. Use this skill when the user needs Guide developers through setting up development environments with proper tools, dependencies, and configurations and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

environment-setup-guide-v3

diegosouzapw/awesome-omni-skills

Environment Setup Guide workflow skill. Use this skill when the user needs Guide developers through setting up development environments with proper tools, dependencies, and configurations and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

environment-specification

yogsoth-ai/de-anthropocentric-research-engine

SOP: define complete experiment environment specification

environmental-geography

Tibsfox/gsd-skill-creator

Human modification of Earth's systems and the geographic dimensions of environmental change. Covers climate change science (greenhouse effect, feedback loops, projections), deforestation and land use change, desertification and soil degradation, water resource management, biodiversity loss and conservation geography, pollution and environmental justice, and sustainability frameworks. Use when reasoning about human impacts on the environment, environmental policy, conservation planning, climate adaptation, or the spatial distribution of environmental risks.

environmental-justice

Tibsfox/gsd-skill-creator

Distributional analysis of environmental benefits and burdens across communities. Covers the historical origins of environmental justice in the U.S. civil rights tradition, siting and exposure disparities, indigenous rights and land stewardship, climate justice at global and intergenerational scales, procedural vs. distributional vs. recognition justice, and the environmental justice screening tools used by regulators. Use when analyzing who bears environmental harm and who receives environmental benefit, or when designing interventions whose distributional consequences matter.

environmental-monitoring

datadrivenconstruction/DDC_Skills_for_AI_Agents_in_Construction

Monitor environmental conditions on construction sites. Track air quality, noise levels, vibration, dust, and weather to ensure compliance and worker safety.

environmental-scanning-foresight

lyndonkl/claude

Monitors external trends across PESTLE dimensions, detects weak signals of emerging change, develops scenario-based futures, and sets adaptive signposts for early warning. Use when scanning external trends for strategic planning, detecting early indicators of change, planning scenarios for multiple futures, setting signposts and indicators for early warning, or when user mentions environmental scanning, horizon scanning, trend analysis, scenario planning, strategic foresight, or futures thinking.

envoy

TerminalSkills/skills

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enzyme_engineering

InternScience/scp

Enzyme Active Site Engineering - Engineer enzyme: identify active site residues, predict pocket, analyze binding site, and predict mutations. Use this skill for enzymology tasks involving predict functional residue run fpocket get binding site by id pred mutant sequence. Combines 4 tools from 3 SCP server(s).

enzyme_inhibitor_design

InternScience/scp

Enzyme Inhibitor Design - Design enzyme inhibitor: target structure, pocket prediction, compound screening, and ADMET assessment. Use this skill for enzyme pharmacology tasks involving retrieve protein data by pdbcode pred pocket prank quick molecule docking pred molecule admet calculate mol drug chemistry. Combines 5 tools from 2 SCP server(s).

eodhd-apis-automation

ComposioHQ/awesome-claude-skills

"Automate Eodhd Apis tasks via Rube MCP (Composio). Always search tools first for current schemas."

eol-communication

borghei/Claude-Skills

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eol-message

deanpeters/Product-Manager-Skills

Write a clear, empathetic EOL announcement with rationale, customer impact, and next steps. Use when retiring a product, feature, or plan without creating avoidable confusion.

epf-build

SteelMorgan/1c-agent-based-dev-framework

Собрать EPF/ERF из XML-исходников. Используй после внесения временных диагностических правок в разобранную обработку.

epf-dump

SteelMorgan/1c-agent-based-dev-framework

Разобрать EPF/ERF в XML-исходники. Используй, когда нужно быстро получить исходный код внешней обработки или отчета для анализа и временной модификации.

epf-operations

SteelMorgan/1c-agent-based-dev-framework

Операции с внешними обработками 1С (EPF) — создание, добавление форм и шаблонов. Используй при epf init, add-form, add-template, add-attribute, add-tabular-section.

epf-validate

SteelMorgan/1c-agent-based-dev-framework

Валидация внешней обработки 1С (EPF). Используй после создания или модификации обработки для проверки корректности

epic-breakdown-advisor

deanpeters/Product-Manager-Skills

Break down epics into user stories with Humanizing Work split patterns. Use when a backlog item is too large to estimate, sequence, or deliver safely.

epic-design

alirezarezvani/claude-skills

Use for any landing page, hero section or scroll-driven web design that should feel cinematic (parallax, scrollytelling, overlapping sections, text reveals, Apple-style animation), before coding. Inspects assets with inspect-assets.py, then builds with 45+ 2.5D techniques, no WebGL.

epic-games-automation

ComposioHQ/awesome-claude-skills

"Automate Epic Games tasks via Rube MCP (Composio). Always search tools first for current schemas."

epic-hypothesis

deanpeters/Product-Manager-Skills

Frame an epic as a testable hypothesis with target user, expected outcome, and validation method. Use when defining a major initiative before roadmap, discovery, or delivery planning.

epicenter-ui

EpicenterHQ/epicenter

Epicenter UI component selection and composition patterns for Svelte apps using packages/ui. Use when choosing or reviewing @epicenter/ui components, loading states, empty states, skeletons, spinners, command empty states, action pending UI, table/list no-row states, button tooltips, wrapper minimization, or replacing ad hoc UI such as Loading... text, custom loading dots, raw animate-pulse placeholders, or one-off centered status markup.

epidemiological-genomics-amr-surveillance

swaruplab/operon

Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.

epidemiological-genomics-pathogen-typing

swaruplab/operon

Assigns isolate identity at the right resolution for the question -- ANI / Mash species triage, 7-locus MLST historical comparability, cgMLST / wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom SeqSphere, EnteroBase HierCC), in-silico serotyping (SISTR, SeqSero2 for Salmonella; SerotypeFinder for E. coli; Kaptive K/O for Klebsiella; SeroBA for pneumococcus; spa + SCCmec for S. aureus), and lineage callers (TB-Profiler / Mykrobe Coll-Napier barcode for MTBC, Pangolin + Nextclade for SARS-CoV-2, PopPUNK GPSC for S. pneumoniae). Use when typing bacterial isolates for surveillance or outbreak investigation, choosing between cgMLST allele distance and core-SNP distance for cluster definition, harmonising calls across schemas / database versions (chewBBACA vs Ridom vs EnteroBase), assigning MTBC lineage with the Napier 2020 90-SNP barcode, calling Salmonella serovar via SISTR with monophasic Typhimurium awareness, running Pangolin UShER mode with explicit pangolin-data version pinning, or selecting a typing resolution to match the surveillance question.

epidemiological-genomics-phylodynamics

swaruplab/operon

Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

epidemiological-genomics-transmission-inference

swaruplab/operon

Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

epidemiological-genomics-variant-surveillance

swaruplab/operon

Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage fitness modelling (Wenseleers / Bedford-Figgins multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data version pinning (mandatory for reproducibility), Nextclade dataset versioning (lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme version churn (V3 / V4 / V4.1 / V5.3.2 / Midnight 1200) with documented dropout regions, recombinant X-prefix Pango designation lag, GISAID vs INSDC dual-deposition tensions, and the Karthikeyan 2022 wastewater early-detection signal with explicit reproducibility caveats. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater pooled samples into lineage frequencies with Freyja, tracking lineage frequencies and growth advantages over time, pinning pangolin-data / Nextclade dataset versions for reproducibility, handling ARTIC primer dropouts (V4.1 amplicons 64 / 76 / 88-90), or running variant surveillance for SARS-CoV-2 / influenza / Mpox / RSV / H5N1 / measles.

epidemiology

mkurman/zorai

Disease modeling and epidemiological analysis: SIR/SEIR compartmental models, R0 estimation, outbreak simulation, incidence/prevalence forecasting, and intervention impact modeling.

epigenetics_drug

InternScience/scp

Epigenetics & Drug Response - Link epigenetics to drug response: gene regulation, variant effects, drug interactions, and expression. Use this skill for epigenetic pharmacology tasks involving get overlap region get vep hgvs get drug interactions by drug name get gene expression across cancers. Combines 4 tools from 3 SCP server(s).

epigenomic_landscape

InternScience/scp

Epigenomic Landscape Mapping - Map epigenomic landscape: overlapping features, regulatory elements, binding matrices, and phenotype links. Use this skill for epigenomics tasks involving get overlap region get phenotype region get species binding matrix get track data. Combines 4 tools from 2 SCP server(s).

epigenomics-methylgpt-agent

swaruplab/operon

AI-powered DNA methylation analysis using MethylGPT foundation models for epigenomic profiling, differential methylation detection, and cancer epigenome characterization.

epigraphdb-skill

openai/plugins

Submit compact EpiGraphDB API requests for ontology, literature, MR, gene-drug, and support-path evidence. Use when a user wants concise EpiGraphDB summaries

epistemology

Tibsfox/gsd-skill-creator

Theory of knowledge and justification across the Western philosophical tradition. Covers the tripartite analysis (justified true belief), Gettier problems, foundationalism vs. coherentism vs. reliabilism, skepticism (Cartesian and external world), rationalism vs. empiricism, Kant's synthesis, social and feminist epistemology, pragmatist epistemology, naturalized epistemology, and philosophy of science (Popper, Kuhn, Lakatos, Feyerabend). Use when analyzing claims about knowledge, evidence, certainty, justification, or scientific method.