Results for “sample”

Runs a sample in an instrumented sandbox to observe behavior: process tree, file and registry changes, network activity, and persistence, then summarizes the behavioral report into capabilities and IOCs. Activates for requests to detonate a sample, do dynamic or behavioral analysis, or interpret sandbox output.

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Bypasses anti-VM and sandbox checks during analysis by locating the specific detection routines (artifact strings, timing, CPUID/hypervisor bit) and planning patches or environment hardening so the sample detonates. Activates for requests to bypass anti-VM checks, defeat sandbox detection, or make an evasive sample run for analysis.

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Analyzes the PE Rich header and related compiler artifacts to fingerprint the build toolchain, cluster related samples, and detect inconsistencies that suggest tampering. Activates for requests to analyze a Rich header, fingerprint the compiler/linker, or cluster samples by build toolchain.

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Detects sandbox and analysis evasion techniques in a sample by scanning static strings, imports, and API traces for VM artifact checks, timing/sleep stalls, anti-debug calls, and environment fingerprinting. Activates for requests to detect sandbox evasion, find anti-VM or anti-debug checks, or explain why a sample did not detonate.

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Research, author, validate, render, and archive data-only Pulp Sample Heritage profiles. Use when creating or revising a sampler character profile, importing or exporting Heritage JSON, proving profile behavior with analytic and listening fixtures, recording evidence and trademark-safe provenance, or preparing a caller-owned profile artifact bundle.

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Validate, install, update, list, rescan, remove, and reveal data-only Pulp content packs for installed plugins. Use for presets, themes, samples, sample banks, wavetables, and other end-user data that must be reviewed before install or update.

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Generate a fully customized Amazon Connect AI agent PoC bundle (Lambda handlers, OpenAPI spec, AI agent prompt, Contact Flows, CloudFormation/CDK infrastructure, FAQ knowledge base) from a ~15-minute structured interview — or from a requirements doc, a flow sketch, or an existing flow/prompt you want to improve. Use when the user wants to build, scaffold, prototype, or refine an Amazon Connect contact center, an AI voice/chat agent on Amazon Connect, or any contact-center use case that mentions Connect, Lex, Wisdom, Q in Connect, "AI agent domain", or Agentic CX Designer (ACXD, Connect Customer, the Agentic CX block — the ACXD runtime target). Also triggers on "I have a requirements document", "turn this flow sketch into a Contact Flow", or "improve my existing Contact Flow / AI prompt". Produces 6 asset packages on local disk.

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Generate a fully customized Amazon Connect AI agent PoC bundle (Lambda handlers, OpenAPI spec, AI agent prompt, Contact Flows, CloudFormation/CDK infrastructure, FAQ knowledge base) from a ~15-minute structured interview — or from a requirements doc, a flow sketch, or an existing flow/prompt you want to improve. Triggers on "amazon connect", "aicc", "contact center AI", "connect ai agent", "connect ai agents domain", "agentic cx designer", "acxd", "connect customer", "agentic cx block", "requirements document", "improve my contact flow", "flow sketch", "\uc544\ub9c8\uc874 \ucee4\ub125\ud2b8", "\ucee8\ud0dd\uc13c\ud130 AI \uc0c1\ub2f4\uc6d0".

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Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal correlation, chromatin state segmentation, enhancer-gene linkage, or any analysis that requires merging or comparing data from two or more ENCODE experiments. Covers same-assay cross-sample, multi-omic same-sample, cross-organism, and perturbation integration designs. Guides compatibility checks, batch effect detection, normalization, integration strategy selection, and provenance documentation.

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Design and evaluate paid-ad experiments with hypotheses, randomization units, sample-size and duration assumptions, guardrails, platform experiment tools, analysis, and decision rules. Use for A/B test, split test, experiment design, hypothesis, statistical significance, sample size, test duration, or experiment readout.

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Build sample/demo screens that make library options explorable. Add controls, previews, presets, sample data, and QA surfaces in the app module.

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Calculate statistical power and sample sizes for RCTs. Use when user mentions: power analysis, sample size calculation, minimum detectable effect, MDE, statistical power, effect size, clustering effects, design effect, ICC, intra-cluster correlation.

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Create new skills, modify and improve existing skills, and measure skill quality. Use when users want to create a skill from scratch, edit or refine an existing skill, test a skill with sample prompts, or optimize a skill's description for better triggering accuracy.

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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reassembly + PairHMM mechanism (why HC beats pileup callers on indels), the -ERC GVCF reference-confidence model and <NON_REF> allele, BQSR-vs-DRAGSTR and --dragen-mode error modeling, allele-specific (AS_) annotations, and edge cases (ploidy, Mutect2 mitochondria mode, sex chromosomes/PAR, contamination gating). Use when deciding whether to use HaplotypeCaller vs a pileup or DRAGEN caller, whether BQSR still earns its place, whether to call per-sample GVCFs for a cohort, or how to handle non-diploid, mitochondrial, sex-chromosome, or contaminated samples. Not for post-calling filtering depth (see variant-calling/filtering-best-practices) or cohort joint-genotyping scaling (see variant-calling/joint-calling).

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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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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.

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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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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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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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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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