「detecting」の検索結果

Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.

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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kortel 2021), GLORI (Liu 2023, antibody-free chemical conversion), DART-seq (Meyer 2019, APOBEC1-YTH fusion), m6Anet (nanopore direct RNA), or MeRIP-seq with calibration. Use when distinguishing antibody-based from antibody-free m6A detection methods, applying the DRACH motif constraint, reconciling cross-method disagreements (DART 44% in DRACH vs GLORI), or detecting m6Am at the cap.

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Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma, Schwede & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2021 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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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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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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Access Core Motion accelerometer, gyroscope, magnetometer, device-motion, pedometer, activity-recognition, altitude, headphone motion, batched high-frequency workout motion, and water-submersion/depth data. Use when reading device sensors, counting steps, detecting walking/running/driving/cycling, tracking altitude, building motion interactions, handling AirPods head tracking, or implementing watchOS dive/depth features.

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Verify device legitimacy and app integrity using DeviceCheck (DCDevice per-device bits) and App Attest (DCAppAttestService key generation, attestation, and assertion flows). Use when implementing fraud prevention, detecting compromised devices, validating app authenticity with Apple's servers, protecting sensitive API endpoints with attested requests, or adding device verification to a backend architecture.

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Load this first for any task involving images, pictures, photos, scans, frames, volumes, or visual data — including reading, writing, filtering, enhancing, denoising, sharpening, deblurring, thresholding, segmenting, masking, detecting, finding or counting objects, removing backgrounds, measuring, comparing, registering, stitching, aligning, cropping, resizing, transforming, or analyzing. Use for image I/O (TIFF, PNG, JPEG, RAW, HDR), histograms, edge detection, color processing, morphology, geometric transforms, deep learning for images, quality assessment, and 3-D volume processing. Also triggers when users describe image problems (dark, noisy, blurry, low contrast, uneven lighting, hazy, color cast) or data exploration tasks (folder of images, characterize data, understand format). Handles microscopy (cells, particles) and general scientific imaging. Routes to sibling skills for medical imaging (DICOM, NIfTI), hyperspectral data, and visual inspection.

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Check and compare software component versions on SageMaker HyperPod cluster nodes - NVIDIA drivers, CUDA toolkit, cuDNN, NCCL, EFA, AWS OFI NCCL, GDRCopy, MPI, Neuron SDK (Trainium/Inferentia), Python, and PyTorch. Use when checking component versions, verifying CUDA/driver compatibility, detecting version mismatches across nodes, planning upgrades, documenting cluster configuration, or troubleshooting version-related issues on HyperPod. Triggers on requests about versions, compatibility, component checks, or upgrade planning for HyperPod clusters.

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Adversarial verification for AI-generated legal content. Use when fact-checking legal documents, validating citations, detecting hallucinations, scoring document quality, or assessing distribution readiness.

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Audit UI/UX designs for quality, AI-generated slop, and accessibility. Use when reviewing designs, detecting slop patterns, validating WCAG compliance, checking design-token adherence, or reviewing responsive design across breakpoints.

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Audit data quality across pipelines, warehouses, and stores. Use when designing a DQ program, defining DQ dimensions, building rule-based checks, detecting schema drift, monitoring freshness SLAs, or responding to a DQ incident.

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IoT network traffic analyzer for detecting IoT protocols and identifying security vulnerabilities in network communications. Use when you need to analyze network traffic, identify IoT protocols, or assess network security of IoT devices.

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Use when detecting and running project build systems automatically. Supports npm/yarn/pnpm/pip/poetry/gradle/maven/cargo/go/make. Triggers on build, test run, project setup, package manager detection.

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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression

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This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

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Amazon competitor monitoring and competitive intelligence for sellers. Track pricing changes, inventory levels, new product launches, review velocity, and advertising patterns for competitor ASINs. Set up monitoring alerts for price drops, stock-outs, and market changes. Works on 12 Amazon marketplaces. No API key required. Use when: (1) monitoring competitor pricing strategies, (2) tracking competitor inventory and stock patterns, (3) detecting new product launches in your category, (4) analyzing competitor review velocity and ratings, (5) identifying market opportunities from competitor gaps, (6) setting up competitive alerts and benchmarks.

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Audit structural debt, logic leakage, and monolithic components across Web, Mobile, and Backend codebases. Use when reviewing architecture, assessing tech debt, detecting logic in wrong layers, or identifying God classes.

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This skill should be used when the user asks to "verify a fix", "reproduce failure", "diagnose issue", "check BEFORE/AFTER state", "VF task", "reality check", "check test quality", "mock-only tests", or needs guidance on verifying fixes by reproducing failures before and after implementation, or detecting mock-heavy test anti-patterns.

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Creates custom Semgrep rules for detecting security vulnerabilities, bug patterns, and code patterns. Use when writing Semgrep rules or building custom static analysis detections.

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Map code questions to the optimal tldr command by detecting intent and routing to the right analysis layer.

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