「sat」の検索結果

Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and 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 (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding. Covers pegRNA design with PRIDICT and PRIDICT2 (Mathis 2023/2024) for predicting per-pegRNA editing efficiency, pegRNA architecture (spacer + scaffold + PBS + RTT), PE2 / PE3 / PE3b / PEmax / PEAR variants, MOSAIC in situ saturation mutagenesis (Hsu JY et al 2024 bioRxiv), the PRIME pooled-screen methodology (Erwood/Doman 2023 Nat Biotechnol 41:885; ~3,699 ClinVar variant screens), chromatin context as a primary determinant of PE efficiency, scaffold-incorporation and indel byproduct quantification with CRISPResso2, and the cross-modal validation strategy of PE + base-editor screens for variant function. Use when designing a pegRNA library for variant installation, choosing between BE and PE for a specific edit, predicting pegRNA efficiency before library synthesis, analyzing PE screen output, distinguishing intended-edit from scaffold-incorporation, or scaling PE screens to thousands of variants.

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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), MSIngs, MANTIS, MSIPanel, MSIDetect, and ngsMSI for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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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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Estimate 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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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.

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Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional estimand reporting per FDA 2023 covariate adjustment guidance, g-computation/standardisation for marginal effects, modified Poisson for RR, Brant test for proportional odds, Firth penalty for separation, and Hauck-Donner detection. Use when modeling binary or ordinal endpoints in confirmatory or exploratory clinical trials.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Provides distributed transaction patterns using the Saga Pattern for Spring Boot microservices. Use when implementing distributed transactions across services, handling compensating transactions, ensuring eventual consistency, or building choreography or orchestration-based sagas with Kafka, RabbitMQ, or Axon Framework.

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Read this skill before the first step of any request to do something in an app on the person's own computer (Notes, Finder, System Settings, any desktop app), to look at their screen, or for "computer use". Computer use (desktop control) lets Claude take screenshots of the person's desktop and control it with clicks, typing and scrolling through the Claude desktop app; its tools are named mcp__computer-use__* when the session runs in the desktop app and mcp__remote-devices__computer_* when a cloud session is linked to the person's computer; before computer use is turned on for a conversation there may be no such tools, only an enable__mcp__remote-devices__computer tool, which turns it on. It covers turning it on, picking the right tool, the access flow, and the safety rules for tiered apps, links and financial actions. It is not for websites, which go through Claude in Chrome or the built-in browser and their own skills.

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Import a memory export from another AI assistant into Claude's memory — conversationally, additively, and with the content treated as data.

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Azure AI VoiceLive SDK for Java. Real-time bidirectional voice conversations with AI assistants using WebSocket.

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A playful, energetic, cartoonesque interface inspired by friendly children's-book illustrations — warm cream backgrounds, big bold custom display typography, saturated brand color blocks, thick black outlines, generously rounded shapes

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Conversational AI-first interface with minimal controls, clear outcomes, and delegated task flows for agentic workflows.

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Reconcile SDD Composy task Markdown and the JSON projection: read-only inspect and plan, then apply only with an explicit authority and the CONFIRM-SDD-SYNC token. Use when task contracts and operational state diverged — 'sincronizar as tarefas', 'o JSON das tasks está desatualizado', 'markdown and json disagree'. Do NOT use to list or advance tasks (sdd-tasks), for a status overview (sdd-status), or to simulate approval.

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Use when starting any conversation in a repository that uses PWDEV Power - establishes how to find and apply Power skills before any response, including clarifying questions

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Triage application logs, open GitHub issues, pending feedback, in-app Issues, and agent conversations. Runs five phases: logs → close shipped issues → feedback → in-app issues → agent FAQ gaps. Use when /whats shows pending feedback, checking app logs, cleaning up shipped issues, or working the in-app Issues backlog.

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Codify the most recent successful /scrape flow into a permanent browser-skill on disk. Future /scrape calls with the same intent run the codified script in ~200ms instead of re-driving the page. Walks back through the conversation, synthesizes script.ts + script.test.ts + fixture, runs the test in a temp dir, and asks before committing. Use when asked to "skillify", "codify", "save this scrape", or "make this permanent". (gstack)

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Self-tuning question sensitivity + developer psychographic for gstack (v1: observational). Review which AskUserQuestion prompts fire across gstack skills, set per-question preferences (never-ask / always-ask / ask-only-for-one-way), inspect the dual-track profile (what you declared vs what your behavior suggests), and enable/disable question tuning. Conversational interface — no CLI syntax required. Use when asked to "tune questions", "stop asking me that", "too many questions", "show my profile", "what questions have I been asked", "show my vibe", "developer profile", or "turn off question tuning". (gstack) Proactively suggest when the user says the same gstack question has come up before, or when they explicitly override a recommendation for the Nth time.

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Turn the current conversation context into a PRD draft. Use when user wants to create a PRD from the current context; publish it to an issue tracker only after explicit approval.

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Turn the current conversation context into a PRD and publish it to the project issue tracker. Use when user wants to create a PRD from the current context.

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