674 件 ・ 関連度順
概要と使いどころ
Plans and executes GKE cluster creation, provisioning, and production readiness audits using pre-defined templates (Autopilot, Standard Regional, GPU/AI Inference, AI Hypercompute). Use when creating GKE clusters, provisioning GKE environments, selecting cluster modes, or auditing GKE clusters. Don't use for application onboarding or deployment configuration (use gke-app-onboarding instead).
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Context is the complete state available to a language model at inference time. It includes everything the model can attend to when generating responses: system instructions, tool definitions, retrieved documents, message history, and tool outputs.
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Audit agent runtimes and their tests for lifecycle inference, capability overload, context pollution, correlated verification, prompt-only control, false success, dead compatibility paths, test-only seams, and complexity without contribution. Use for whole-repository agent audits, slop or dead-code triage, test contribution reviews, large refactors, tool/context simplification, and cleanup requests that need proof before deleting code or tests.
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Causal inference with treatment/control groups over time. Use when user mentions: treatment effects, policy evaluation, pre/post comparison, parallel trends, DID, DiD, difference in differences, natural experiment, quasi-experimental.
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Design randomized controlled trials for causal inference. Use when user mentions: randomized evaluation, RCT, field experiment, randomized experiment, treatment assignment, causal impact, experimental design, control group, intervention evaluation.
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Naturalistic causal reasoning for failures and disputed attribution. Use when postmortems or root-cause debates need reframing. NOT for causal inference, fault trees, or fully observed failures.
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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.
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Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the critique that "n=3" is a publication convention rather than a power calculation. Use when budgeting a sequencing experiment, writing the sample-size justification in a grant, estimating replicates from pilot data, allocating a fixed budget between samples and depth, or planning scRNA-seq cohort size. For clinical-trial sample size see clinical-biostatistics/power-and-sample-size; for the power-given-n direction see experimental-design/power-analysis.
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Detects m6A modifications from Oxford Nanopore direct-RNA-seq (DRS) signal using m6Anet (multiple-instance-learning over DRACH 5-mer signal). Covers the upstream pipeline (Dorado/Guppy basecalling -> minimap2 map-ont -> nanopolish eventalign -> m6anet dataprep -> m6anet inference), per-site vs per-read probability including the mod_ratio stoichiometry column, the DRACH-only constraint, minimum-coverage thresholds (20-50 reads/site), multi-condition comparison via xPore/Nanocompore/ELIGOS, Dorado native modification calling (RNA004, 2024+), and the cDNA-vs-DRS distinction (cDNA Nanopore CANNOT detect modifications). Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting probability_modified vs mod_ratio vs per-read probabilities, deciding between m6Anet (known DRACH sites) and Dorado/Remora (genome-wide screening), pinning RNA002 vs RNA004 chemistry and basecaller versions, or troubleshooting eventalign/dataprep failures.
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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.
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Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, 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; MRSA <=15; C. difficile <=2; Klebsiella <=21), models within-host diversity and transmission bottlenecks, integrates contact-tracing data, distinguishes generation from serial interval, and attributes source via Bayesian source attribution (islandR). 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 a 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 or chronic HIV.
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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with 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 models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.
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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.
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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.
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Estimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).
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Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.
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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
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Capture what someone actually said without contaminating it with your own inference. Invoke when eliciting intent in conversation (design discussion, requirement interview, decision surfacing) and when turning a conversation into a durable record (ADR, decision node, memory entry, spec `## Decisions` row). Enforces quote-before-critique, keeps illustration separate from commitment, and holds interpretation subordinate to verbatim. Prevents the failure where unspecified space is filled by the recorder and then evaluated as if the speaker had specified it.
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Audits GitHub Actions workflows for security vulnerabilities in AI agent integrations including Claude Code Action, Gemini CLI, OpenAI Codex, and GitHub AI Inference. Detects attack vectors where attacker-controlled input reaches. AI agents running in CI/CD pipelines.
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llama.cpp local GGUF inference + HF Hub model discovery.
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Expert-level statistics knowledge. Use when working with probability distributions, hypothesis testing, regression, Bayesian statistics, statistical inference, experimental design, ANOVA, or statistical modeling. Also use when the user mentions 'p-value', 'confidence interval', 'hypothesis test', 'regression', 'ANOVA', 'chi-square', 't-test', 'Bayesian', 'maximum likelihood', 'statistical significance', 'correlation', 'normal distribution', or 'sampling distribution'.
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Build AI agents with Hugging Face's SmolAgents framework. Use when creating code-executing agents, tool-calling agents, multi-agent systems, agentic RAG, text-to-SQL pipelines, web browsing agents, or any multi-step AI workflows. Covers CodeAgent, ToolCallingAgent, custom tools, MCP integration, memory management, secure code execution (E2B, Docker, Blaxel), and model configuration (HF Inference, LiteLLM, Transformers, Ollama).
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When shaping feedback — situation-behavior-impact, growth-vs-corrective split, cadence design, ladder-of-inference checks. Triggers on 'how do I give this feedback', 'perf review shape'.
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