Results for “sample”

Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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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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Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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Estimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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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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Read, write, and query Apple Health data using HealthKit. Covers HKHealthStore authorization, sample queries, statistics queries, statistics collection queries for charts, saving HKQuantitySample data, background delivery, workout sessions with HKWorkoutSession and HKLiveWorkoutBuilder, HKUnit, and HKQuantityTypeIdentifier values. Use when integrating with Apple Health, displaying health metrics, recording workouts, or enabling background health data delivery.

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Transmit and capture RF waveforms using Wireless Testbench with NI USRP radios (X410, X310, N310, N320, N321, N300, X300, E320). Use when generating test signals, transmitting over the air, capturing IQ data, performing loopback tests, configuring multi-antenna setups, or troubleshooting dropped samples and gain settings. Covers basebandTransceiver, basebandTransmitter, basebandReceiver, continuous and once transmit modes, foreground and background capture, and UseRadioBuffer options. Also use when the user mentions transmit waveform, capture signal, IQ data, loopback, RF gain, sample rate, or antenna configuration.

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Generate database seed scripts with realistic sample data. Reads Drizzle schemas or SQL migrations, respects foreign key ordering, produces idempotent TypeScript or SQL seed files. Handles D1 batch limits, unique constraints, and domain-appropriate data. Use when populating dev/demo/test databases. Triggers: 'seed database', 'seed data', 'sample data', 'populate database', 'db seed', 'test data', 'demo data', 'generate fixtures'.

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Clinical study operations — protocol structure, endpoint selection, eligibility design, sample-size and power planning, site feasibility, and documentation readiness. Use when planning, auditing, or costing a study.

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This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and qua

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We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experi

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Design, plan, and analyze A/B tests with statistical rigor. Use when the user asks about A/B testing, split testing, experiment design, statistical significance, sample size calculation, test duration, multivariate testing, or conversion experiments. Trigger phrases include "A/B test", "split test", "experiment", "statistical significance", "sample size", "test duration", "which version wins", "conversion experiment", "hypothesis test", "variant testing".

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结构化数据分层采样工具。读取 JSONL、JSON、CSV、TSV、XLSX、XLS 等结构化数据，按指定字段分层后无放回抽取样本，输出保留原字段结构的采样结果。 当用户提到分层采样、类别平衡采样、按标签抽样、训练集分层划分等需求时使用此skill。 即使用户没有明确说出"stratified_sampler"，只要任务涉及按字段分层并进行代表性抽样，就应该使用此skill。 不负责随机采样、领域均衡采样、批量切分、时间窗口抽样或格式转换。

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JSONL 随机采样工具。读取 JSONL 数据集，按抽样数量或抽样比例无放回抽取样本，输出保留原字段结构的采样结果。 当用户提到随机采样、按数量抽样、按比例抽样、JSONL 抽样筛查等需求时使用此skill。 即使用户没有明确说出"random_sampler"，只要任务涉及对 JSONL 记录做无放回随机抽取，就应该使用此skill。 不负责分层采样、领域均衡采样、表格采样或其他格式转换。

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Inspects videos, extracts frames, and concatenates video clips stored in Volcengine TOS: read video metadata, capture single snapshots, batch-capture multiple frames by explicit timestamps or interval, concatenate multiple video clips, and save results locally or back to TOS. Use this skill when the user needs to get video duration or codec info, capture a poster image or thumbnail, extract frames at specific timestamps, sample frames at regular intervals, merge or join multiple video clips into one — even if they don't explicitly mention 'video processing' or 'frame extraction'.

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Use when the user wants to analyze dataset bias, create stratified samples, evaluate fairness, or plan dataset collection. Triggers on phrases like "dataset bias", "stratified sample", "class imbalance", "data distribution", "fairness analysis", or "ethical review".

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Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).

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Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples. Handles strandedness (0/1/2), paired-end, multi-sample batch counting in one command, and outputs assignment statistics. Use Salmon for alignment-free quantification; use featureCounts when STAR BAMs already exist.

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Use when data needs statistical analysis. Runs reproducible Python/R code for Table 1, diagnostic accuracy, agreement, regression, survival, propensity score, survey-weighted and repeated-measures models, with publication tables. Sample size is /calc-sample-size; pooling studies is /meta-analysis.

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Build consistent characters, environments and props in Guaardvark's Cast Library and train LoRAs for them locally (reference photos → vision bible → sample plan → approved samples → training). Use when the user wants the same face or object across images, videos, a music video, or a Film Crew production, or asks to "train a LoRA".

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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