「assess」の検索結果

Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.

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Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA pembrolizumab pan-tumor 2020.

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Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Predicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES gold-standard endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Map owned assets, attack surface, and inventory for systems the requester is authorized to assess. Use for asset discovery, service catalogs, and exposure reviews — never unauthorized scanning.

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Evaluate design from a UX perspective, assessing visual hierarchy, information architecture, emotional resonance, cognitive load, and overall quality with quantitative scoring, persona-based testing, and actionable feedback. Use when the user asks to review, critique, evaluate, or give feedback on a design or component.

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Testing and benchmarking LLM agents including behavioral testing, capability assessment, reliability metrics, and production monitoring—where even top agents achieve less than 50% on real-world benchmarks

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This skill should be used when the user asks to "implement LLM-as-judge", "compare model outputs", "create evaluation rubrics", "mitigate evaluation bias", or mentions direct scoring, pairwise comparison, position bias, evaluation pipelines, or automated quality assessment.

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Use this skill when the user requests to review, analyze, critique, or summarize academic papers, research articles, preprints, or scientific publications. Supports comprehensive structured reviews covering methodology assessment, contribution evaluation, literature positioning, and constructive feedback generation. Trigger on queries involving paper URLs, uploaded PDFs, arXiv links, or requests like "review this paper", "analyze this research", "summarize this study", or "write a peer review".

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Use when the user wants to review a pull request, understand what a PR changes, assess risk of merging, or check for missing test coverage. Examples: "Review this PR", "What does PR #42 change?", "Is this PR safe to merge?"

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Assess release readiness from applicable criteria, all current defects, risks, limitations, and recorded human decisions without approving release.

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Use when a user asks for QA planning, execution, review, release assessment, reporting, status, or test-tool recommendations and the correct PWDEV QA workflow must be selected safely.

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。

Assess requirement clarity, testability, completeness, consistency, and traceability without inventing missing acceptance criteria.

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Review a code diff or explicit file set through independent correctness and QA lenses. Use when the user asks for a code review, test-coverage assessment, pre-merge audit, or review gate in a PWDEV Flow workflow.

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Diagnose repository and PWDEV Flow health without changing the project. Use when the user asks for a health check, workspace consistency check, dependency assessment, readiness report, or evidence-based scorecard.

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Evaluate an interface from a UX perspective, assessing hierarchy, information architecture, emotional resonance, cognitive load, and overall quality with evidence-linked judgments and actionable feedback. Use when the user wants an overall design or UX review—not when the main need is measurable accessibility/performance diagnosis, or final micro-detail polish.

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Systematically review pull requests, feature implementations, and code changes to ensure quality, maintainability, security, and adherence to best practices. Use when reviewing code before merging, conducting peer reviews, performing self-reviews, auditing code quality, checking for security vulnerabilities, ensuring consistent coding standards, verifying test coverage, assessing performance implications, evaluating architectural decisions, or providing constructive feedback to improve team code quality.

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Extract actionable skill knowledge from academic papers and research articles, assess credibility, run security checks, and either improve existing skills or create new ones. Load when the user asks to learn from a paper, extract insights from a research paper, turn a paper into a skill, apply paper findings to skills, read this paper and improve my skills, or process a research article. Also triggers on "skill from paper", "learn from this paper", "paper to skill", "extract from this research", "apply this paper", or when the user uploads or links to an academic PDF or paper URL.

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Extract actionable insights from blog posts, web articles, and practitioner content - assess credibility, run security checks, and either improve existing skills or apply to the current project. Load when the user asks to learn from an article, extract insights from a blog post, apply a practitioner's findings, or process engineering blog content. Also triggers on "learn from this article", "learn from this blog post", "extract insights from this post", "what can we learn from this article", "apply this article", or when the user links to a blog, Medium, Substack, dev.to, or engineering blog post.

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Extract actionable patterns, architecture decisions, code conventions, and skill-relevant insights from GitHub/GitLab repositories. Assess repo credibility, run the full security scan pipeline, and apply findings to existing skills, new skills, or the current project. Load when the user asks to learn from a repo, extract patterns from a codebase, study a repository, or analyze a repo for reusable techniques. Also triggers on "learn from this repo", "learn from this repository", "what can we learn from this codebase", "extract patterns from this repo", "study this repo".

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。