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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.
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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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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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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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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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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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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
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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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Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end 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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Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
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Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
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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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Analyze AMS waveform data using Mixed-Signal Blockset utilities: phase noise measurement, clock jitter, anti-aliased resampling, timing measurements, lock time, INL/DNL, ADC/DAC calibration, HSpice import. Use when analyzing time-domain voltage from PLL/VCO/clock simulations, measuring phase noise from variable-step solver output, computing jitter, or resampling non-uniform data.
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Merge two pages that describe the same thing, preserving every distinct claim, redirecting inbound links, and recording the merge. Use this skill when the user approves a duplicate merge, says "these are the same page", "merge X into Y", or asks to clean up near-duplicates that a lint run proposed. Do NOT use to merge pages on your own judgement, to delete a page outright, or to split one page into several.
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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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Market sizing and market structure work — TAM/SAM/SOM built top-down and bottom-up then reconciled, segmentation, demand triangulation, and survey design. Use when sizing a market, writing a sizing memo, or fielding a survey.
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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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Analyzes how multiple regulations interact for a specific product, service, or business model. Identifies where obligations overlap, reinforce, complement, duplicate, or conflict; builds a priority matrix; produces an integrated compliance timeline; and estimates the total compliance burden. Use when (1) scoping a new product or service against the full regulatory landscape before launch, (2) conducting M&A due diligence on a target's multi-regulation exposure, (3) building a strategic compliance roadmap where single-regulation analyses miss the interactions, (4) advising on complex situations where regulations touch the same conduct from different angles, or (5) estimating budget and resourcing for multi-regulation compliance. Primary coverage of EU digital regulation (GDPR, Data Act, AI Act, CRA, NIS2, DORA, DMA, DSA, ePrivacy) and national implementations; the framework extends to any jurisdiction where overlapping regulatory regimes apply to the same activity.
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Deep market analysis for iOS/macOS apps including market sizing (TAM/SAM/SOM), growth trends, market maturity, entry barriers, distribution channels, and revenue potential. Use when user asks for market research, market size, market opportunity, growth potential, TAM/SAM/SOM, or market trends.
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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
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。