'analyse' 검색 결과

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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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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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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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

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Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA 2023 covariate adjustment guidance. Covers Table 1 generation, analysis populations (ITT/FAS/PP/Safety), the 5 ICH E9(R1) intercurrent-event strategies, MMRM under MAR (mmrm), reference-based MI (rbmi J2R/CR/CIR), Permutt tipping-point sensitivity, and Rubin's-rules vs frequentist variance debate. Use when preparing regulatory submissions, defining estimands, or implementing missing-data sensitivity analyses.

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Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submissions or precision-medicine claims.

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Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-based multiple imputation (J2R, CR, CIR, LMCF per Carpenter-Roger 2013), Permutt delta-adjustment / tipping-point analysis, pattern-mixture identifying restrictions (CCMV, NCMV, ACMV), and the Cro vs Bartlett variance debate. Use when handling missing primary or secondary endpoint data in regulatory submissions following NRC 2010 and ICH E9(R1).

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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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DraftForge PR lifecycle workflow. Use when the user runs /pr, opens or pushes a pull request, or asks to monitor CI checks and Copilot review on a branch. Creates the PR (or reuses an existing one), polls GitHub Actions and Copilot up to ~15 min, then analyses CI failures and Copilot comments and reports findings grouped by file and skill.

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Remove signs of AI-generated writing from text. Use when editing or reviewing text to make it sound more natural and human-written. Based on Wikipedia's comprehensive "Signs of AI writing" guide. Detects and fixes patterns including: inflated symbolism, promotional language, superficial -ing analyses, vague attributions, em dash overuse, rule of three, AI vocabulary words, negative parallelisms, and excessive conjunctive phrases. Credits: Original skill by @blader - https://github.com/blader/humanizer

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Re-run the analysis pipeline on all runs matching an RQ, reaggregate metrics, and propose findings updates against the fresh data. Trigger when the user says "reanalyze RQ-N", "reanalyse RQ-N", "Runs neu analysieren", or wants to refresh metrics/findings after a pipeline change (analyze-run.sh fix, adapter added, ESLint config).

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Apply to any non-trivial work, not just bulk work: edits, migrations, analyses, checks. Build the tool that does it or proves it (codemod, script, generator, or a skill your subagents follow) instead of working by hand. The tool is the artifact a reviewer can rerun.

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Generate formal IT/hardware purchase request documents from informal requirements. Use when creating purchase justifications, cost-benefit analyses, ROI calculations, vendor comparisons, or MARP presentation slides for management approval.

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Review audit-related documents (control design documents, bottleneck analyses, requirements definitions, etc.) for quality, scoring them 0-100 with a severity-rated findings list. Use when reviewing audit documents, checking control design quality, or verifying cross-document consistency. Supports documents governed by US GAAP, IFRS, or J-GAAP.

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Namespace router → the four-axis health and integrity audit, read through four dimensions of agent movement (change point, jurisdiction, invariant, escalation). Use when the operator reports that gzkit feels "wobbly", misaligned, or that governance is not holding — or before a release, to check that declared mechanisms still fire. Routes to the concrete axis surfaces in a fixed cheapest-first order; owns the ordering rationale, the reading frame and the budget rule, not the analyses themselves.

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Prepares the trend update for a recurring emailed report: identifies report emails not yet processed, extracts the configured metrics from their spreadsheet, CSV or PDF attachments, returns new rows for an append-only trends sheet and writes a DRAFT summary with period-on-period deltas and flagged anomalies. Use when the user asks to "update the trends for the weekly report", "analyse the latest monthly report", "what changed in the latest report", "do the latest numbers look unusual" or "set up tracking for a report that arrives by email". Do not use for a single file with no trend state, use dataset-insight-pack instead. Drafts for human review; never approves, authorises or signs off.

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Synthesises training survey responses and manager notes into a DRAFT training needs report by role: coded needs with record counts per role (n of N), the evidence type behind each count, anonymised quotes cited to record codes, disagreements between what staff report and what managers observe, gaps where a role is under-represented or a required skill has no evidence, and follow-up questions to settle before any course is designed. Never rates an individual, ranks a team or turns a count into a competence verdict. Use when the user asks to "analyse this training survey", "what training do our teams need", "summarise the manager feedback on skills gaps", "build a training needs analysis by role" or "which roles have the biggest skill gaps". Do not use for turning an agreed need into a course, use course-outline-builder instead; for exit interviews, use exit-interview-synthesis. Drafts for human review; never approves, authorises or signs off.

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Synthesises exit interview notes or leaver survey responses into a DRAFT themed report: coded themes with record counts and shares, anonymised verbatim evidence, breakdowns by broad group only for groups that meet a minimum group size, referred items and open questions for the people team, without naming or identifying any individual. Use when the user asks to analyse, summarise, code, theme or report on exit interviews, leaver feedback, attrition interviews or departure surveys, or says "what are our leavers telling us", "theme these exit interviews" or "summarise the leaver survey". Do not use for customer or product feedback, use customer-feedback-theme-synthesis instead; for redacting one document with no theming, use document-deidentification-pass. Drafts for human review; never approves, authorises or signs off.

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Builds a DRAFT quiz from the training content the user supplies (slide deck, manual, e-learning script, session transcript, procedure): numbered questions with the correct answer, distractors drawn from the content itself, an explanation quoting the source passage with its location, a difficulty tag (Recall, Apply, Analyse) with its basis, and a coverage table showing which sections and objectives each question tests and which are left uncovered. Use when the user asks to "build a quiz from this deck", "write knowledge check questions for this module", "create an assessment from this training", "test understanding of this procedure" or "which sections does this quiz cover". Do not use for a reader-facing question and answer page built from documents, use faq-builder instead; for writing the procedure itself from notes or a walkthrough, use sop-drafter. Drafts for human review; never approves, authorises or signs off.

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Reads one spreadsheet, CSV export or pasted table together with the user's question and drafts an insight pack: a data profile, observations cited to named columns and values and framed as leads, caveats, and suggested charts and follow-up analyses. Every figure carries the label "as read, verify in source"; correlation is never stated as causation. Use when the user asks to "profile this spreadsheet", "what does this data say", "find anomalies in this extract", "give me a first read on this CSV" or "summarise this table". Do not use for a purchase order log or spend extract, use purchase-order-anomaly-review instead; for actuals versus budget, use budget-variance-explainer instead; for a report that arrives by email on a schedule, use report-attachment-analyzer instead. Drafts for human review; never approves, authorises or signs off.

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Synthesises a batch of customer feedback (survey answers, reviews, ticket and chat comments) into a DRAFT themed report: coded themes with record counts and shares, anonymised verbatim quotes cited to record codes, contradictions and unverified claims, and the follow-up questions to answer next. Produces no sentiment score or percentage positive as fact; ratings appear only as distributions with n. Use when the user asks to "theme this feedback", "what are customers saying", "summarise these survey answers", "analyse these reviews", "find the top complaints in these comments" or "code this voice of the customer data". Do not use for exit interviews, use exit-interview-synthesis instead; for sorting a live queue and drafting replies, use ticket-triage-pack; for project retrospectives, use lessons-learned-synthesis. Drafts for human review; never approves, authorises or signs off.

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Use when evaluating, designing, drafting, revising, stress-testing, or preparing academic articles, empirical research reports, literature reviews, systematic reviews, meta-analyses, journal submissions, reviewer responses, research methods, sampling, measurement, analysis, publication readiness, or citation/source audits.

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