67건 · 관련도순
Parses and processes SARIF files from static analysis tools like CodeQL, Semgrep, or other scanners. Triggers on "parse sarif", "read scan results", "aggregate findings", "deduplicate alerts", or "process sarif output". Handles filtering, deduplication, format conversion, and CI/CD integration of SARIF data. Does NOT run scans — use the Semgrep or CodeQL skills for that.
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Own concrete MSBuild ItemGroup and item-expression questions. USE FOR: Include, Remove, Update, item identity and metadata, transforms, filtering, batching, duplicate or overlapping items, and reviews that verify whether those operations are correct. Generated items stay in scope when the central defect is item identity, metadata, batching, duplicate declarations, or glob/Remove/Update semantics. For a generated artifact missing from compilation or output, wrong target timing/path, or FileWrites clean tracking without a broader item-semantics defect, use including-generated-files. The item operation may be broken, suspected, or already correct. Exclude property-only issues, general incrementality with no item question, broad reviews with no concrete item concern, and non-MSBuild systems.
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Guide CUDA-enabled BindCraft protein-binder design from target PDB preparation through AF2/MPNN/PyRosetta execution, filtering, output analysis, and conservative troubleshooting.
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Collect, normalize, and structure execution traces from instrumented programs (strace, ltrace) into JSON format for downstream analysis. Use when working with system call traces, library call traces, or execution logs that need to be analyzed for debugging, test case reproduction, or verification. Supports parsing strace/ltrace output, filtering noise, extracting debug information, and preparing traces for bug analysis or reproduction workflows.
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Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. Use when starting a proteomics analysis with raw or processed MS data. Handles contaminant filtering and missing value assessment.
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Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
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Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or RFdiffusion outputs, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding success rates, (5) Need better ranking than ipTM or iPAE. For structure prediction, use chai or alphafold. For QC thresholds, use protein-qc.
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Build content filtering for AI outputs. TRIGGERS - Use when user needs help with ai-content-filter related tasks.
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Use the hyalo CLI instead of read/edit/grep/write when working with markdown (.md) files that have YAML frontmatter. This skill MUST be consulted whenever pi is working with markdown documentation directories, knowledgebases, wikis, notes, Obsidian-compatible collections, Zettelkasten systems, iteration plans, or any collection of .md files with frontmatter. Trigger this skill when: searching or filtering markdown files by content, tags, or properties; reading or modifying YAML frontmatter; managing tags or metadata across documents; toggling task checkboxes in markdown; getting an overview of a documentation directory; querying document properties or status fields; bulk-updating metadata across many markdown files; or when you find yourself repeatedly using read/edit/grep/write on .md files. Even if the user does not mention "hyalo" by name, use this skill whenever the task involves structured markdown documents with frontmatter. For pi sessions, ALWAYS use `--format text` for compact, LLM-friendly output.
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Apply these opinionated testing conventions whenever writing, reviewing, or planning tests: what earns a test and what is coverage theatre, asserting outputs rather than mock calls, the three modes (functional, performance, security), naming and isolation rules, where to mock, and reporting findings for coverage rather than self-filtering. Includes house Jest standards for NestJS unit and contract tests, TDD discipline, and test-report structure.
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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.
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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
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Use when running verbose CLI commands — wraps them with rtk (Rust Token Killer, third-party Apache-2.0; upstream reports 60-90% token savings). Covers installation, configuration, and usage patterns.
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Patterns for managing MSBuild item groups: Include/Remove/Update semantics, item metadata, batching with %(Metadata), transforms, per-item filtering, and cross-product batching pitfalls. Only activate in MSBuild/.NET build context. USE FOR: diagnosing and fixing item group anti-patterns in .csproj files, reviewing item management for correctness, fixing CS2002 duplicate file warnings from SDK globbing, fixing targets that run more times than expected due to cross-product batching, fixing Include vs Update misuse on SDK-globbed items, fixing FileWrites registration for generated file clean support, moving generated files to IntermediateOutputPath. DO NOT USE FOR: target chain architecture (use target-authoring), property patterns (use property-patterns), incrementality (use incremental-build), general anti-patterns (use msbuild-antipatterns), non-MSBuild build systems.
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Build content filtering for AI outputs. TRIGGERS - Use when user needs help with ai-content-filter related tasks.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.