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Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

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Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.

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Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus strategy.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Use this skill when the user asks about weigh-station bypass services — Drivewyze, PrePass, BestPass, NORPASS, OOIDA toll savings — how they work, eligibility criteria, costs, and how they tie into CSA scores. Reference each provider's coverage area + pricing.

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Use this skill when the user asks about trucking insurance — types of coverage (commercial auto, cargo, occupational accident, workers comp, bobtail/non-trucking, MCS-90 endorsement), federal minimums (49 CFR 387), what each covers, owner-operator vs company-driver implications, and how to read a Certificate of Insurance (COI). Cite 49 CFR 387.

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Use this skill when the user asks about Household Goods (HHG) movers — 49 CFR 375 + 376 consumer protection rules, FMCSA HHG-specific authority, mover certification, binding vs non-binding estimates, dispute resolution, weight ticket requirements, valuation coverage, and how HHG operations differ from general freight. Cite 49 CFR 375.

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Designs and audits data retention and file compaction for an embedded SQLite datastore in a long-lived service — a unified retention registry (one declared policy per table), TTL / absolute-age / row-count-cap policies, a fail-loud coverage guard, WAL/checkpoint tuning, and auto_vacuum/incremental-vacuum so pruning actually shrinks the file. Use when a SQLite DB grows unbounded, a table has an index but no DELETE, a pruned DB never shrinks on disk, metrics are stored as raw events forever, or a new table needs bounding. Keywords retention policy, TTL, reaper, prune, VACUUM, auto_vacuum, incremental_vacuum, WAL checkpoint, freelist, DB bloat, row cap, per-tenant quota. NOT for Postgres/MySQL/server-DB partitioning or TTL, log-line rate-limiting/sampling, backup/replication, schema migrations, or query-performance indexing.

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Designs or reviews provenance-bound DAG attempt traces, coverage gaps, cancellation, and unknown-effect reconciliation. NOT for claiming execution completeness, deployment monitoring, or root-cause proof.

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Ranks eligible skill candidates with explicit retrieval evidence, capability coverage, and uncertainty. NOT for discovery, authorization, or execution planning.

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Produces a narrow-interval quality signal for a WinDAGs skill that a third party can verify without inspecting model weights or method internals. The mechanism is attribution-kNN over a tamper-evident outcome log (task→skills→accept/reject store), combined with a conformal-prediction calibration certificate that provides a formal coverage guarantee. Thompson/Beta sampling is explicitly rejected as a category error: it produces a selection signal for stationary i.i.d. rewards, not an attestation signal for context-dependent LLM output quality. The resulting bundle — outcome-log Merkle root + conformal threshold + optional TEE guardrail signature — constitutes a "narrow-interval trust" credential: verifiable, bounded, and internals-opaque.

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Verify every visual-evidence artifact (screenshot/GIF/recording) attached to a PR carries a provenance manifest binding it to real daemon-backed truth — daemon port, run id, transcript head hash, agent node id, commit, and an honest real/fixture/mock source label — and that operator-control-panel PRs cover the required set of proof states. Use when gating a PR's proof artifacts before merge, auditing whether a "LIVE" visual claim is backed by a real daemon run versus a reused or fixture-backed mock, or defining the required state-coverage set for a control-panel change. NOT for the capture technique itself — headless Playwright, `screencapture -x -l`, non-interruptive capture (use port-daddy-agent-skill's visual-evidence doctrine), designing the receipt body schema an artifact attaches to (use agent-work-receipt-designer), or the broader dogfood/Potemkin product-quality bar (use multi-agent-authoring-product-bar).

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Analyze a Coval accent testing report from runs across different speaker accents. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or metric summary and wants evidence-backed next steps such as prompt changes, STT/confirmation adjustments, accent-robust routing, or expanded accent coverage.

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Analyze a Coval audio-quality testing report from runs across different voice, speaking-style, volume, interruption, and background-noise scenarios. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or metric summary and wants evidence-backed next steps such as prompt changes, tool handling fixes, STT/TTS adjustments, trace setup, or expanded audio-scenario coverage.

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Analyze a Coval adversarial / red-team testing report and turn it into an agent-hardening plan. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or a per-scenario scorecard from an adversarial sweep and wants evidence-backed next steps such as prompt/guardrail changes, refusal hardening, verification fixes, escalation routing, or expanded attack coverage.

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Build a compact Coval test set from product requirements, observed conversation failures or a coverage gap. Design realistic scenarios with separate expected behaviors, provenance and controlled voice/persona variation.

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Audit an existing Coval evaluation setup for coverage, misleading scores, missing evidence, judge validation and execution risk. Read-only; use when inheriting an eval or deciding whether its results support a release decision.

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Run the pytest test suite with coverage. Accepts optional filter flags. Use after making changes to verify nothing broke.

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Profound LLM citation tracker (extension). Time-series brand citation rates across ChatGPT, Perplexity, and other LLMs. Pairs with seo-seranking for triangulated AI visibility coverage.

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