Results for “data framework”

Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniverse, implement new API integrations, create tool wrappers for scientific databases/services, expand ToolUniverse capabilities, or follow ToolUniverse contribution guidelines. Supports creating tool classes, JSON configurations, validation, error handling, and test examples.

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Work on the dashboard's frontend — the vanilla JS/CSS page with no framework or bundler. Use this whenever a task touches `static/nowplaying.js`, `static/style.css`, the Jinja templates (`templates/nowplaying.html`, `_icons.html`), the accent-color tinting, the karaoke lyrics sync, the now-playing poll, or the empty-state mosaic / recent-plays pile. Covers how the page is wired, how it reads i18n and data from the server, the ESLint gate, and the Android bridge, so changes match the existing patterns.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.

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Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submissions or precision-medicine claims.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Provides guidance for LLM post-training with RL using slime, a Megatron+SGLang framework. Use when training GLM models, implementing custom data generation workflows, or needing tight Megatron-LM integration for RL scaling.

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Master modern business analysis with AI-powered analytics, real-time dashboards, and data-driven insights. Build comprehensive KPI frameworks, predictive models, and strategic recommendations.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.

The English summary is being prepared. Showing the original description.

Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submissions or precision-medicine claims.

The English summary is being prepared. Showing the original description.

Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

The English summary is being prepared. Showing the original description.

Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Architecture and systems design for agents that retain bounded state across sessions. Covers durable event history, owned state, derived memory, retrieval indexes, framework evaluation, recovery, deletion, and rebuild behavior. Uses constructed implementation examples and workload calibration rather than universal vendor, latency, similarity, retention, or cost claims. Activate on: "always-on agent", "persistent agent architecture", "episodic memory system", "agent memory design", "long-running agent", "stateful agent", "agent that remembers", "MemGPT architecture", "Letta deployment", "/always-on-agent-architecture". NOT for: choosing what data to feed the agent (use always-on-agent-inputs), brainstorming applications (use always-on-agent-applications), safety and privacy concerns (use always-on-agent-safety), general agentic patterns (use agentic-patterns).

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Expert guidance for developing cross-platform desktop applications with Avalonia UI framework. Use when building, debugging, or optimizing Avalonia apps including MVVM architecture, XAML design, data binding, styling, theming, custom controls, and cross-platform deployment for Windows, macOS, Linux, iOS, Android, and WebAssembly.

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Patterns and techniques for adding governance, safety, and trust controls to AI agent systems. Use this skill when: - Building AI agents that call external tools (APIs, databases, file systems) - Implementing policy-based access controls for agent tool usage - Adding semantic intent classification to detect dangerous prompts - Creating trust scoring systems for multi-agent workflows - Building audit trails for agent actions and decisions - Enforcing rate limits, content filters, or tool restrictions on agents - Working with any agent framework (PydanticAI, CrewAI, OpenAI Agents, LangChain, AutoGen)

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Provides guidance for LLM post-training with RL using slime, a Megatron+SGLang framework. Use when training GLM models, implementing custom data generation workflows, or needing tight Megatron-LM integration for RL scaling.

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Public-records OSINT investigation framework — SEC EDGAR filings, USAspending contracts, Senate lobbying, OFAC sanctions, ICIJ offshore leaks, NYC property records (ACRIS), OpenCorporates registries, CourtListener court records, Wayback Machine archives, Wikipedia + Wikidata, GDELT news monitoring. Entity resolution across sources, cross-link analysis, timing correlation, evidence chains. Python stdlib only.

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Master modern business analysis with AI-powered analytics, real-time dashboards, and data-driven insights. Build comprehensive KPI frameworks, predictive models, and strategic recommendations. Use PROACTIVELY for business intelligence or strategic analysis.

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Collects and synthesizes open-source intelligence (OSINT) about threat actors, malicious infrastructure, and attack campaigns using publicly available data sources, passive reconnaissance tools, and dark web monitoring. Use when investigating external threat actor infrastructure, performing pre-engagement reconnaissance for authorized red team assessments, or enriching CTI reports with publicly available adversary context. Activates for requests involving Maltego, Shodan, OSINT framework, SpiderFoot, or infrastructure reconnaissance.

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Map advanced persistent threat (APT) group tactics, techniques, and procedures (TTPs) to the MITRE ATT&CK framework using the ATT&CK Navigator and attackcti Python library. The analyst queries STIX/TAXII data for group-technique associations, generates Navigator layer files for visualization, and compares defensive coverage against adversary profiles. Activates for requests involving APT TTP mapping, ATT&CK Navigator layers, threat actor profiling, or MITRE technique coverage analysis.

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Analyzes RAM memory dumps from compromised systems using the Volatility framework to identify malicious processes, injected code, network connections, loaded modules, and extracted credentials. Supports Windows, Linux, and macOS memory forensics. Activates for requests involving memory forensics, RAM analysis, volatile data examination, process injection detection, or memory-resident malware investigation.

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Structured OSINT methodology framework: target definition, source selection, collection workflows, data correlation, timeline reconstruction, and reporting. Use to guide systematic OSINT campaigns or teach OSINT methodology.

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