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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or EarlGrey (auto-curating wrapper), and quantifies TE expression from RNA-seq with TEtranscripts/SQuIRE. Covers de-novo-library-as-curation-project, soft-vs-hard masking, the domesticated-gene over-masking massacre, Dfam-vs-RepBase, TE classification (Class I/II, family-vs-copy), Kimura repeat landscapes, LAI, and the RNA-seq multimapping problem. Use when masking repeats before gene prediction, building a TE library for a non-model genome, or analyzing transposable-element content or expression.

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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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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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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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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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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Use when the user mentions App Store screenshot validation, screenshot review, checking screenshots before submission, or verifying screenshot dimensions and content.

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Use when accepting ANY real-world payment — Apple Pay, Wallet passes, Tap to Pay, Orders in Wallet. NOT in-app purchase / digital content (use axiom-integration). Covers entitlements, certs, signing, App Review payment rules.

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Use when working with ANY GPU rendering, Metal, OpenGL migration, shaders, 3D content, RealityKit, AR, USD/USDZ files, or display performance. Covers Metal migration, shader conversion, RealityKit ECS, RealityView, USDKit, ProMotion.

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Create a reusable SkillPack from a successful completed task. Use when the user wants to convert a one-off research, coding, analysis, or content workflow into a distributable local SkillPack with `skillpack.json`, local skills under `skills/`, starter prompts, start scripts, and an optional zip package.

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Embeds and controls web content in SwiftUI with WebKit for SwiftUI, including WebView, WebPage, navigation policies, JavaScript execution, observable page state, link interception, local HTML or data loading, and custom URL schemes. Use when building iOS 26+ article/detail views, help centers, in-app documentation, or other embedded web experiences backed by HTML, CSS, and JavaScript.

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Build iOS augmented reality and 3D experiences with RealityKit and ARKit. Use when adding RealityView content, loading entities or USDZ models, anchoring objects to planes or world positions, distinguishing entity hit tests from ARKit real-world raycasts, handling AR camera availability, world tracking, scene updates, or RealityKit entity gestures and interactions.

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Add Apple Pencil drawing with PKCanvasView, PKToolPicker, PKDrawing serialization/export, stroke inspection, and PencilKit/PaperKit handoffs. Use when building drawing apps, annotation features, handwriting capture, signature fields, content-version-safe ink workflows, or Apple Pencil-powered experiences on iOS/iPadOS/visionOS.

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Build alternative browser engines using BrowserEngineKit. Use when developing a non-WebKit browser engine for iOS/iPadOS in supported regions, managing web content/rendering/networking extension processes, configuring GPU and networking process capabilities, checking alternative-engine device eligibility, or reviewing BrowserEngineKit entitlements and Info.plist setup.

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Crawl websites (news, blogs, papers, GitHub, product docs, RSS feeds) into a fixed-schema JSONL file, then create a dataset and a searchable application in Viking AI Search. Supports one-time crawl and scheduled recurring crawl with automatic incremental sync.

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Create and edit presentation slide decks (`.pptx`) with PptxGenJS, bundled layout helpers, and render/validation utilities. Use when tasks involve building a new PowerPoint deck, recreating slides from screenshots/PDFs/reference decks, modifying slide content while preserving editable output, adding charts/diagrams/visuals, or diagnosing layout issues such as overflow, overlaps, and font substitution.

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Use when the user or agent needs to read, search, or look up Stripe documentation or API reference. Prefer this over curl or WebFetch for any docs.stripe.com content. Use to fetch gated documentation.

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Use when reviewing a page or site for organic search, or diagnosing why something isn't ranking: crawl and index signals, on-page elements, content quality, and how to order the fixes.

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This skill should be used when creating Ultralytics-branded content of any kind, including PDF, PPTX, Canva, or Google Slides presentations, DOCX documents, marketing or newsletter HTML emails, social media post copy or visuals, website or landing page designs, and dataset or model result visuals. Provides official colors, typography, logo rules, naming rules, and tone of voice from ultralytics.com/brand.

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Use when planning many similar pages from a template and a data set: choosing the pattern, deciding whether the data can carry it, and avoiding the thin-content failure that gets page sets deindexed.

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Agent-browser usage guide. Read this before running any agent-browser commands. Covers the snapshot-and-ref workflow, navigating pages, interacting with elements (click, fill, type, select), extracting text and data, taking screenshots, managing tabs, handling forms and auth, waiting for content, running multiple browser sessions in parallel, and troubleshooting common failures. Use when the user asks to interact with a website, fill a form, click something, extract data, take a screenshot, log into a site, test a web app, or automate any browser task.

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Perform time-frequency analysis in MATLAB using CWT, STFT, synchrosqueezing, reassignment, wavelet coherence, cross spectrogram, EMD/VMD, multiresolution analysis, and time-frequency filtering. Triggers on: time-frequency, spectrogram, scalogram, cwt, stft, istft, fsst, wsst, wcoherence, xspectrogram, modwt, modwtmra, modwpt, emd, vmd, hht, tffilt, dgt, gabor, instantaneous frequency, synchrosqueezing, reassignment, ridge extraction, wavelet coherence, cross spectrum, mode decomposition, signal decomposition, time-frequency filtering.

日本語の概要は準備中です。原文の説明を表示しています。