「enrichment」の検索結果

Use when you need Liberty91 platform intelligence — what actually happened (deduplicated Threat Events with every source, Admiralty reliability/credibility and verification stage), whether an IOC is already known to your account, the canonical threat library (actors, malware, vulnerabilities, clusters, ATT&CK TTPs), alert matches, or which of your customer organizations an occurrence affects — or when you need to push intelligence back: ingesting your own report, generating an intelligence package, or uploading an organization document. Also supplies event provenance fields, when the platform returns them, and Threat Library alias resolution to /source-provenance and /quality-of-information-check. Two-way, first-party integration. Commonly invoked by /ip-investigation and friends, /ioc-enrichment-workflow, /threat-actor-profiling, /campaign-tracking and /vulnerability-intelligence. Reads $LIBERTY91_API_KEY.

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Use when you need to check an IP, domain, file hash, or URL against VirusTotal's reputation database. Returns detection ratio, verdict, community score, and key findings. Commonly invoked by investigation skills (/ip-investigation, /domain-investigation, /hash-investigation, /url-investigation) and by analysts enriching IOCs. Other agents/skills can chain this for VirusTotal enrichment.

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Use when you need authoritative classification, threat-name, MITRE ATT&CK mapping, dynamic-analysis or sandbox results on a file hash, or when you need network threat intelligence for a URL/domain/IP from ReversingLabs Spectra Analyze (A1000). Returns verdict, risk score, AV detection ratio, threat name, behavioural tags, and pivot candidates (parent containers, extracted files, related samples by family). Commonly invoked by /hash-investigation and /malware-analysis. Other agents/skills can chain this for deeper malware enrichment beyond VirusTotal.

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Research a prospect then draft personalized outreach. Uses web research by default, supercharged with enrichment and CRM. Trigger with "draft outreach to [person/company]", "write cold email to [prospect]", "reach out to [name]".

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Research a company or person and get actionable sales intel. Works standalone with web search, supercharged when you connect enrichment tools or your CRM. Trigger with "research [company]", "look up [person]", "intel on [prospect]", "who is [name] at [company]", or "tell me about [company]".

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Enriches indicators with context from threat-intel sources: planning lookups against reputation, passive DNS, WHOIS, and sandbox/sample databases, scoring confidence, and avoiding operational-security mistakes that tip off adversaries. Activates for requests to enrich IOCs, add threat context, or plan indicator lookups safely.

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Client reporting, quality assurance, and financial operations management. Handles KPI frameworks, compliance audits, budget tracking, and launch checklists. Use when: managing client dashboards, ensuring brand compliance, conducting QA reviews, tracking marketing spend, ensuring GDPR/CAN-SPAM compliance, handling a request to delete someone's data across the marketing stack, deciding whether an AI voice or AI presenter has to be disclosed, proofreading deliverables. Also triggers on: client reporting, QA, quality assurance, brand compliance, marketing budget, financial tracking, legal compliance, GDPR, CAN-SPAM, proofreading, launch checklist, right to erasure, right to be forgotten, data deletion request, DSAR, someone asked us to delete their data, do we delete or suppress, suppression list, they unsubscribed and we emailed them again, we deleted them and they came back, restored a backup and re-emailed people, custom audience still has deleted contacts, California Delete Act, DROP, data broker deletion, enrichment records disappearing

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Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models, cross-reference with clinical trials and drug databases, or conduct any disease-focused, pathology-driven, or clinical variant interpretation workflow. Covers the full pipeline from disease-tissue mapping through GWAS variant annotation, heritability enrichment, cancer epigenomics, drug target identification, and clinical trial cross-referencing. Integrates ENCODE with Open Targets, PubMed, ClinicalTrials.gov, and bioRxiv.

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Evaluate ENCODE experiment quality using standard metrics and audit flags. Use when the user asks about data quality, wants to filter for high-quality experiments, needs to interpret quality metrics (FRiP, NSC, RSC, NRF, IDR, TSS enrichment, fragment size), wants to understand ENCODE audit warnings, needs to compare quality across experiments, or is deciding whether data is usable for their analysis. Also use when the user mentions QC, quality control, or data filtering.

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Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif database, binding profile, PWM, position weight matrix, TF motif, motif enrichment, motif scanning, binding site prediction.

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Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and which transcription factors control them?" by layering expression, chromatin accessibility, histone marks, and TF binding data. Follows the Mawla et al. 2023 framework for cross-assay integration of islet cell type-specific data. Handles chromatin state annotation (ChromHMM), enhancer-gene linkage, TF motif enrichment, and cell type-specific regulatory element identification. Use for ANY multi-omic analysis, enhancer discovery, regulatory network construction, or epigenomic characterization using ENCODE data.

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Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosome-free fragment selection. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS enrichment.

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Analyze internal link structure by crawling a domain. Identifies orphan pages, underlinked pages (configurable heuristic, default fewer than 3 inbound links), and broken internal links. Suggests anchor text for top 5 underlinked pages. Reuses existing fetch/parse scripts. Optional Ahrefs enrichment. Use when user says "internal links", "link structure", "orphan pages", "internal linking", "link graph", "anchor text audit".

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Bulk RNA-seq differential expression — experimental design, count modeling with DESeq2/edgeR, and enrichment.

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The GraphQL pipeline for SKMTC generators — authoring generators whose input schema is GraphQL SDL rather than OpenAPI. Covers `toGqlOperationEntry`, `GqlOperation`, `synthesizeArgsObject` (mutation args -> object schema), the GQL enrichment routing (`[id][rootKind][fieldName][variant]` — two nested subject keys where OAS has path+method), the `to<Lang>GqlOperationProjectionBase` companion factories, and the `GeneratorKey` shape `id|rootKind|fieldName|variant`. Use this skill ALONGSIDE `skmtc-generator` whenever the schema source is GraphQL SDL or the task mentions "GraphQL", "SDL", "GqlOperation", "toGqlOperationEntry", or GraphQL query/mutation generators. Engine rules (producers, register/insert, the axioms) stay in `skmtc-generator`; this skill carries only what differs for GraphQL.

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Author and edit Skmtc generators — packages that project an OpenAPI domain model into application code. Method: clone the nearest stock generator, then apply the engine rules imitation can't teach. Assumes zero prior Skmtc knowledge. Use when asked to "write a skmtc generator", "author/clone/customize gen-x", "add a field type", "change export paths", "add enrichment options", or when editing generator source. ALWAYS pair with the target language's skill (skmtc-lang-typescript).

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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.

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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF calibration (BF >6 ≈ 90% posterior per Hart 2017; ~5% FDR by BAGEL convention). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Generate or repair a project's .gitignore. Composes the baseline must-ignore set (the single source of truth in baseline-ignores.json) with optional gitignore.io enrichment, and merges add-only so existing entries are never lost. Use when a repo has no .gitignore, when the commit-leak guard reports a gap, or when onboarding a new stack. Trigger: "set up gitignore", "fix my gitignore", "ignore node_modules/secrets", "gitignore for <stack>".

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