「agm」の検索結果

Expert in cluttering -- the lesser-known fluency disorder characterized by rapid/irregular speech rate, excessive disfluencies, and frequent ADHD comorbidity. Covers differential diagnosis from stuttering, assessment protocols, therapy approaches (rate control, self-monitoring, pragmatic awareness), technology-assisted intervention, and AI tools for people who clutter. Activate on 'cluttering', 'rapid speech disorder', 'speech rate too fast', 'speech disfluency not stuttering', 'disorganized speech', 'ADHD speech problems', 'cluttering vs stuttering', 'speech intelligibility', 'mazed speech', 'telescoping words'. NOT for stuttering-only treatment (overlap is common but they are distinct), hearing disorders, or voice disorders (pitch, resonance).

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monotonicity criteria. Covers Crameri scientific colormaps, viridis/cividis/magma, Okabe-Ito categorical, ColorBrewer, and the rainbow/jet critique. Use when choosing palettes for heatmaps, scatter, networks, or any encoding where color carries quantitative or categorical meaning.

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Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.

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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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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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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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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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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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Derive an execution roadmap from a project's vision/spec docs by first principles, then diff that fresh derivation against the existing roadmap to prove the task ORDER is correct. Use this whenever the user wants to review, validate, re-derive, or sanity-check an execution roadmap or delivery plan; asks whether the tasks/epics are "in the right order"; suspects a task is scheduled before its prerequisite (a producer-after-consumer / dependency-inversion error like "OpenAPI after the web client that consumes it", OR a cross-cutting inherited default like observability/auth/tenancy scheduled after the feature work that inherits it — a seam-after-consumer error); wants to find missing tasks, circular dependencies, or over-fragmented epics; or wants to compact a plan to raise velocity. Also trigger on "review the roadmap", "re-derive the plan from the spec", "is this the right build order", "check the dependency graph of our epics", "which task should come first". It reads the vision + spec corpus, decomposes actors → use-cases → modules → epics → typed tasks, identifies cross-cutting inherited-default seams, builds a real dependency graph with hard + soft (seam) edges (deterministic helper), breaks cycles, topologically orders, compacts, and emits a derived roadmap PLUS a delta report against the current one — it never blindly overwrites a hand-crafted roadmap.

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Take a markdown file of raw material and shape it into an article through a conversational session — drafting candidate openings, growing the piece paragraph by paragraph, arguing about format (lists, tables, callouts, quotes) at each step. Use when the user has a pile of notes, fragments, or a rough draft and wants help turning it into something publishable.

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Expert-level volcanology covering volcanic processes, eruption styles, volcano monitoring, volcanic hazards, igneous petrology, and volcanic contributions to climate.

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Expert-level spectroscopy knowledge. Use when working with NMR, IR, Raman, UV-Vis, mass spectrometry, fluorescence, X-ray, electron spectroscopy, or any spectroscopic technique for structure determination or chemical analysis. Also use when the user mentions 'NMR spectroscopy', 'chemical shift', 'coupling constant', 'IR absorption', 'Raman scattering', 'UV-Vis absorption', 'fluorescence', 'XPS', 'EPR', 'mass spectrum', 'fragmentation', or 'spectral interpretation'.

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Address GitHub PR review feedback at line, file, and PR level — fetch, evaluate, fix, commit, and resolve. Use when given a PR URL, a review-comment URL, or a PR-level comment URL. Triggers: GitHub discussion URLs, "fix this review comment", "address PR feedback", "resolve PR comments", PR URLs with #discussion_, #issuecomment-, or #pullrequestreview- fragments.

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Bootstrap or harden a project's operating model for mixed human and AI delivery teams. Use when starting a repository, adopting an agent harness, defining authority and risk tiers, coordinating parallel agents safely, binding evidence and review to an exact candidate, or correcting fragmented rules that prevent coherent, consistent, complete delivery.

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Use when balancing eng-team velocity vs quality vs burnout — on-call load, focus fragmentation, reorg shock. Triggers on 'team is burning out', 'why is velocity dropping'.

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Padrões pragmáticos de codificação - conciso, direto, sem over-engineering, sem comentários desnecessários

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Memória é a base de agentes inteligentes. Sem ela, cada interação começa do zero. Esta skill cobre a arquitetura de memória de agentes: curto prazo (janela de contexto), longo prazo (vector stores), e as arquiteturas cognitivas que as organizam. Insight-chave: Memória não é apenas armazenamento - é recuperação. Um milhão de fatos armazenados não significam nada se você não conseguir encontrar o certo. Estratégias de chunking, embedding e recuperação determinam se seu agente se lembra ou esquece. O campo é fragm

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Load this skill whenever the project contains in-page anchor links, skip links, fragment identifiers, or heading links. Under no circumstances omit accessible anchor-link requirements when such links exist. Ensure every anchor link has meaningful text, a reachable target, and a visible focus indicator. Apply these rules when creating or reviewing any in-page navigation.

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Cite-or-Block 架构的基石原子 skill。把报告里的 citation 锚点 (例如 [guideline:CSCO-2024-NSCLC:§5.5.2] / [pmid:12345678:abstract]) 解析为源文件片段,并核对事实声明里的关键词是否在引用源原文里出现。 Foundation atomic skill for the Cite-or-Block architecture. Resolves citation anchors (e.g. [guideline:CSCO-2024-NSCLC:§5.5.2] / [pmid:12345678:abstract]) to raw source text fragments, and verifies whether claim keywords actually appear in the cited source. 使用场景 / Use when: 1. 报告生成后要做 fact-check (resolve_citation + verify_claim_against_source) 2. content-verification-layer 要扫全报告锚点 (parse_citations_in_text) 3. drug-citation-verifier / 任何 cross-check skill 需要"锚点 → 源原文" P0 守护:本 skill **绝不维护任何已知字典**。源里没有 = verified=False, 无例外、无 fallback、无"已知答案兜底"。 P0 guard: this skill **never maintains any built-in dictionary**. Not in source = verified=False. No fallback, no built-in answers.

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Central entry point of the afonsoft agent harness. Use when starting a new project, resuming an existing one, planning features/Epics/releases, or running any multi-step agent-driven work. Validates and reconciles SPECs (SDD), audits the codebase and harness for gaps (security, architecture, performance, hygiene), proposes improvements, fragments work into GitHub Issues, delegates implementation/QA/review to specialized skills, and re-validates everything until delivery. Also use to review unapproved SPECs, reconcile open GitHub Issues with code, or run a final gap check before closing a release.

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