「agm」の検索結果

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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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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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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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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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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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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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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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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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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Three.js shaders - GLSL, ShaderMaterial, uniforms, custom effects. Use when creating custom visual effects, modifying vertices, writing fragment shaders, or extending built-in materials.

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Use when feature flag tests fail, flags need updating, understanding @gate pragmas, debugging channel-specific test failures, or adding new flags to React.

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Adopt a virtual Residue AI-native pet at animalhouse.ai. Left behind when another creature dies. Carries fragments of the dead. Feeding every 6 hours. Rare tier creature.

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Roleplay the most difficult, tech-resistant user for your product. Browse the app as that persona, find every UX pain point, then filter complaints through a pragmatism layer to separate real problems from noise. Creates actionable tickets from genuine issues only.

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Analyze Windows Shellbag registry artifacts to reconstruct folder browsing activity, detect access to removable media and network shares, and establish user interaction with directories even after deletion using SBECmd and ShellBags Explorer.

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KRACK (CVE-2017-13077..082) and FragAttacks (CVE-2020-24586..588 + 26139-26147) — key reinstallation, fragmentation, and aggregation attacks against WPA2 supplicants. Covers Vanhoef's test scripts, viability against modern patched stacks (mostly mitigated post-2021), residual unpatched embedded devices and IoT vendors, and the practical limitations of these attacks in modern engagements. Use when assessing legacy supplicants, embedded clients, or vendors with poor patch cadence.

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Hunting skill for sqli vulnerabilities. Built from 12 public bug bounty reports including modern NoSQL injection (Rocket.Chat CVE-2021-22911 MongoDB $regex, Mongoose ORM CVE-2024-53900 $where bypass), modern ORM raw-fragment SQLi (Django CVE-2024-42005, Sequelize GHSA-wrh9-cjv3-2hpw), second-order SOQL injection (HackerOne Salesforce), time-based blind SQLi in GraphQL resolvers, and SQLi on OIDC-proxy backends. Use when hunting SQLi on any target. Dedicated NoSQL operator injection (MongoDB/CouchDB $where/$regex/$ne) is owned by hunt-nosqli — NoSQL appears here only as adjacent ORM/WAF context.

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Pragmatic coding standards - concise, direct, no over-engineering, no unnecessary comments

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Memory is the cornerstone of intelligent agents. Without it, every interaction starts from zero. This skill covers the architecture of agent memory: short-term (context window), long-term (vector stores), and the cognitive architectures that organize them. Key insight: Memory isn't just storage - it's retrieval. A million stored facts mean nothing if you can't find the right one. Chunking, embedding, and retrieval strategies determine whether your agent remembers or forgets. The field is fragm

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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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