「frequency」の検索結果

Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.

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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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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV and AnnotSV for semi-automated scoring. Covers the separate copy-number-loss and copy-number-gain rubrics, the five-tier classification, ClinGen haploinsufficiency/triplosensitivity and dosage-sensitive regions, de novo and segregation evidence, and population-frequency benign evidence. Use when assigning pathogenic/likely-pathogenic/VUS/likely-benign/benign to a constitutional CNV, scoring a CNV against ACMG/ClinGen criteria, or distinguishing the automatable evidence from the case-specific evidence requiring manual input.

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Use this skill to design an annual driver refresher training program. Covers what to cover, frequency, documentation, and ROI.

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Use this skill when a driver needs to extend the 14-hour duty window using the 16-hour exception under § 395.1(o). Covers eligibility, frequency limits (once per 7 days), return-to-terminal requirement, and documentation.

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Use this skill to understand when to update your USDOT number registration (MCS-150). Covers triggers, frequency, and consequences of late updates.

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Build or improve a Coval dashboard with metric visualizations backed by real data. Creates new dashboards from scratch or rebuilds existing ones by analyzing usage patterns, metric frequency, and data density. Use when user says "create a dashboard", "build a dashboard", "improve my dashboard", "add widgets", "visualize my metrics", "make a performance dashboard", or "dashboard for my runs".

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Define analysis steps and procedures. Use when user mentions static analysis, dynamic step, frequency analysis, heat transfer step, or asks about analysis type, time increments, or nlgeom.

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Complete workflow for modal/frequency analysis - extract natural frequencies and mode shapes. Use for vibration analysis and resonance avoidance.

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Detect RDP brute force attacks by analyzing Windows Security Event Logs for failed authentication patterns (Event ID 4625), successful logons after failures (Event ID 4624), NLA failures, and source IP frequency analysis.

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Parse Apache and Nginx access logs to detect SQL injection attempts, local file inclusion, directory traversal, web scanner fingerprints, and brute-force patterns. Uses regex-based pattern matching against OWASP attack signatures, GeoIP enrichment for source attribution, and statistical anomaly detection for request frequency and response size outliers.

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[BETA] AEM Cloud Service expert skill — add explicit connect/read/socket timeouts to outbound HTTP clients constructed without one (Apache HttpClient 4.x/5.x, OkHttp, JDK java.net.http.HttpClient), including the JDK per-request read timeout on HttpRequest. Use for "add HTTP timeouts", "this external/outbound call has no timeout", or a scan that flags a timeout-less client. Highest-frequency CSO outage cause: a client on default (effectively infinite) timeouts holds request threads on a slow upstream until the Jetty pool saturates and the site goes down. The analyzer locates timeout-less construction sites; mechanical per-library remediation applies CSO-backed default timeouts (recipe.md). This skill is in beta. Verify all outputs before applying them to production projects.

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