「composition」の検索結果

Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.

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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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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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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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Analyzes code files and reports statistics including line counts, file counts by extension, and total size. Use this skill whenever the user wants to understand the composition of a codebase - asking about "how many lines of code", "what file types exist", "code distribution", or needing a quick audit of project size and structure. Make sure to invoke this skill when users mention analyzing codebases, counting lines, checking file distributions, or auditing code.

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RF Toolbox and RF Blockset in MATLAB -- S-parameter I/O, network conversions (S/Z/Y/ABCD/T/H/G, mixed-mode), cascade/de-embedding, rfbudget analysis, circuit composition, matching networks, amplifier stability, mixer spurs, rational fitting, SI channels, baseband processing, Circuit Envelope simulation. Trigger: sparameters, Touchstone, .s2p, .s4p, rfplot, smithplot, rfparam, rfwrite, zparameters, yparameters, abcdparameters, s2sdd, cascadesparams, deembedsparams, rfbudget, noise figure, OIP3, IIP3, amplifier, modulator, nport, rffilter, attenuator, seriesRLC, shuntRLC, lcladder, txline, circuit, setports, clone, matchingnetwork, stabilityk, stabilitymu, powergain, gammams, gammaml, mixerIMT, OpenIF, rational, rationalfit, stepresp, txlineWRLGC, rf.Amplifier, rf.Mixer, rf.Filter, rf.Sparameter, rfsystem, RF Blockset.

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Scan package dependencies for known vulnerabilities using Snyk, Dependabot, and OWASP Dependency-Check. Identify and remediate vulnerable libraries in your software supply chain. Use when managing third-party dependencies or implementing software composition analysis.

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Apply step-by-step analysis for complex problems with revision capability. Use for multi-step reasoning, hypothesis verification, adaptive planning, problem decomposition, course correction.

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Product photography for Etsy — composition, lighting, backgrounds, editing, lifestyle shots, 360 views

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Orchestrate iOS screenshot automation with xcodebuild/simctl for build-run, AXe for UI actions, JSON settings and plan files, Koubou-based framing (`asc screenshots frame`), and screenshot upload (`asc screenshots upload`). Use when users ask for automated screenshot capture, AXe-driven simulator flows, frame composition, or screenshot-to-upload pipelines.

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Multi-agent orchestration for complex tasks. Use when tasks require parallel work, multiple agents, or sophisticated coordination. Triggers include requests for features, reviews, refactoring, testing, documentation, or any work that benefits from decomposition into parallel subtasks. This skill defines how to orchestrate work using cc-mirror tasks for persistent dependency tracking and TodoWrite for real-time session visibility.

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Physics-based animation library combining React Spring (spring dynamics, gesture integration, 60fps animations) and Popmotion (low-level composable animation utilities, reactive streams). Use when building fluid, natural-feeling UI animations, gesture-driven interfaces, physics simulations, or spring-loaded interactions. Triggers on tasks involving React Spring hooks, spring physics, inertia scrolling, physics-based motion, animation composition, or natural UI movements. Alternative physics approach to motion-framer for more physically accurate animations.

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Best practices for Remotion - Video creation in React

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Use when creating or revising finished video thumbnails or cover images with Scenario: game trailers, boss reveals, patch updates, devlogs, or community videos needing readable composition, exact headline text and consistent characters. Not for title ideas or critique alone, in-video title cards, or a generic image without a thumbnail deliverable.

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Audit and improve Jetpack Compose runtime performance from code review and architecture. Use when asked to diagnose slow rendering, janky scrolling, excessive recompositions, or performance issues in Compose UI.

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Run a structural-review debate between two lenses — lowy (volatility-based decomposition) and hickey (structural simplicity) — on the current diff. Each reviews independently, then they cross-examine every finding until they agree per-finding, and the agreed fixes are applied. Use when the user types `/lens-debate`, or asks to "have lowy and hickey review this", "run the lens debate", "debate this diff structurally", or "argue the structure of this PR until the lenses agree".

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Best practices for Remotion - Video creation in React

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Builds Vue 3 components with Composition API, configures Nuxt 3 SSR/SSG, sets up Pinia stores, scaffolds Quasar/Capacitor mobile apps, and implements PWA features.

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System decomposition and dependency mapping

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Arbitrator research tool for investor-State dispute settlement (ISDS). The tool can summarize arbitrators' experience, with deliverables grounded in primary documents; it can also help find arbitrators based on the issues faced in a particular case. Use when the user asks about an arbitrator ("tell me about arbitrator X", "X, Y and Z"), wants help choosing or shortlisting arbitrators for a case, or asks about appointments, dissents, issue track records (e.g. FET, expropriation), challenge risk, double-hatting, or tribunal composition. Profiles are grounded in the UNCTAD ISDS Navigator dataset plus targeted live lookups (ICSID); deep verification retrieves the actual decisions. Sibling of isds-research.

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