「nct」の検索結果

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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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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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 16a.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, mixed), Hochberg/Hommel/Holm with PRDS, and the closed-testing principle (Marcus-Peritz-Gabriel; Goeman 2021 admissibility). Covers FDA Multiple Endpoints Final Guidance (October 2022), graphical procedures via R gMCP, primary + key-secondary + subgroup hierarchies, and FWER vs FDR distinction. Use when designing the multiplicity strategy for confirmatory trials with multiple primary or key secondary endpoints.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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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/MntJULiP/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 aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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Implement, review, or improve data visualizations using Swift Charts. Use when building bar, line, area, point, pie, donut, or iOS 26 3D charts; when adding chart selection, scrolling, annotations, axes, scales, legends, or foregroundStyle grouping; when plotting functions with BarPlot, LinePlot, AreaPlot, PointPlot, Chart3D, or SurfacePlot; or when creating heat maps, Gantt charts, grouped bars, sparklines, threshold lines, or spatial visualizations.

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Postgres best practices maintained by Supabase, for Postgres running anywhere. Load this skill BEFORE writing or changing anything that lives in a Postgres database: creating or altering tables and columns (including choosing column types), schema design, migrations and declarative schema files, RLS policies and the tests that verify them, indexes, triggers, database functions, queues and scheduled jobs (pg_cron, pgmq), vector/semantic search (pgvector), and restoring dumps (pg_restore) or importing data. Also load it when diagnosing slow queries, high CPU, timeouts, EXPLAIN plans, connection exhaustion, locking, bloat, or rows visible to the wrong user or tenant. This is not just a performance guide — schema, migration, security, and SQL authoring tasks need these rules too, even for a one-column change or a single query.

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This skill should be used when user asks to "use supabase CLI", "supabase init", "supabase start", "run migrations", "deploy edge functions", "manage Supabase project", or works with the supabase command-line tool for local development and project management.

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Guides MongoDB users through implementing and optimizing Atlas Search (full-text), Vector Search (semantic), and Hybrid Search solutions. Use this skill when users need to build search functionality for text-based queries (autocomplete, fuzzy matching, faceted search), semantic similarity (embeddings, RAG applications), or combined approaches. Also use when users need text containment, substring matching ('contains', 'includes', 'appears in'), case-insensitive or multi-field text search, or filtering across many fields with variable combinations. Provides workflows for selecting the right search type, creating indexes, constructing queries, and optimizing performance using the MongoDB MCP server.

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This skill should be used when user asks to "use supabase-js", "query Supabase database", "supabase auth", "supabase storage", "supabase realtime", "supabase edge functions", or works with the @supabase/supabase-js JavaScript/TypeScript SDK.

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Guidance for distinctive, intentional visual design when building new UI or reshaping an existing one. Helps with aesthetic direction, typography, and making choices that don't read as templated defaults.

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Manage MATLAB packages with the in-product MATLAB Package Manager (mpm) on MATLAB R2026b or later: install, uninstall, update, search, or inspect packages; declare package dependencies in a matlab.toml project; install a shareable .mltbx package; or manage repositories. Covers dependency-resolution errors and anything involving mpminstall / mpmuninstall / mpmupdate / mpmlist / mpmsearch / mpmAddRepository / matlab.mpm.*. MATLAB *packages* are distinct from MathWorks products, toolboxes, and support packages: a bare "what packages are installed?" means MPM packages (mpmlist / matlab.mpm.Package) — this skill — unless the user explicitly says products, toolboxes, or support packages. NOT for installing MATLAB, Simulink, or toolboxes from a shell via the standalone mpm executable (the OS-level product installer), nor for listing installed products / toolboxes (ver, installedAddons) — use matlab-install-products for those.

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Generate standard-compliant IEEE 802.11 waveforms using MATLAB WLAN Toolbox. Use when creating WLAN waveforms, PPDU packets, or the transmit side of a link-level simulation. Covers all formats: Non-HT (802.11a/g), HT (802.11n), VHT (802.11ac), HE-SU/HE-MU/HE-TB (802.11ax), EHT-MU/EHT-TB (802.11be), UHR-MU/UHR-TB/UHR-ELR (802.11bn). Handles single-user, MU-MIMO, OFDMA, trigger-based uplink, extended range, preamble puncturing, UEQM, and DRU. Use when asked to generate test waveforms, create packets with MAC frames, configure OFDMA resource units, build trigger-based uplink transmissions, target a specific transmit duration, or build multi-packet waveforms.

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Discover OPC UA servers, connect MATLAB clients, and browse/navigate server nodes using opcuaserverinfo, the Local Discovery Service (LDS), opcua, connect, setSecurityModel, certificate-trust functions, findNodeById, opcuanode, and Namespace/Children traversal. Use when finding OPC UA servers on the network, querying endpoints and security policies, connecting to a server, authenticating with username/password or certificates, configuring security modes, handling certificate-trust or hostname-mismatch errors, troubleshooting failed connections or empty discovery, inspecting an OPC UA certificate (.der/.pem), browsing an address space, finding nodes by name or NodeId, navigating node hierarchies, invoking method nodes, or batch-processing large namespaces. Trigger on: opcuaserverinfo, LDS, opcua, opc.ua.Client, setSecurityModel, opc.ua.trustServerCertificate, OPC UA certificate, findNodeById, opcuanode, browse OPC UA, find node, OPC UA namespace, OPC UA method node, Industrial Communication Toolbox.

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Read BEFORE writing any code that adds Additive White Gaussian Noise (AWGN) to signals and converts between SNR, Eb/No, Es/No, and per-subcarrier SNR for communications simulations, using awgn(), convertSNR(), berawgn(). The default MATLAB patterns for AWGN (e.g., 'measured' option, manual SNR formulas) produce subtly incorrect results. This skill specifies the correct calling conventions, required function usage, and critical anti-patterns that must be avoided.

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Select and use Audio Toolbox acoustic, psychoacoustic, and speech quality metrics. Use when computing loudness, sharpness, roughness, fluctuation strength, noise criteria (NC/RNC/RC), speech transmission index (STI), speech intelligibility index (SII), speech quality (ViSQOL, STOI), SPL, reverberation time (RT60), tone-to-noise ratio, or prominence ratio. Also use when asked about PESQ, POLQA, calibration factor, EBU R 128, LUFS, HVAC noise, background noise evaluation, or how to measure audio quality or noise compliance. Covers calibration, standard selection, signal alignment, and the complete function inventory including what does NOT exist.

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