“mutation”的搜索结果

修改应用或文件前先核实目标，仅更新所需部分，再重新读取以验证结果。删除或发送时，还会核对操作对象及影响是否在用户指示范围内。

• 仅更新应用中的指定项目
• 确认文件移动或删除的结果
• 检查发送或预约是否执行完成

Analyze candidate sites where sugars may attach to proteins, review experimental evidence, and prepare prediction or structural shielding workflows. Supports mutation planning, antibody glycan comparisons, and interpretation of site-specific measurements while distinguishing candidates from confirmed modifications.

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• Find candidate glycosylation sites in protein sequences
• Plan mutations and rescan altered sequences
• Compare antibody Fc glycoforms

Change a running OpenRig setup by adding or removing agent seats, connecting existing sessions, or attaching terminals. Guides checks for roles, startup context, permissions, and session identity so the setup reflects each change correctly.

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• Add agent seats to a running rig
• Remove seats and clean up remaining references
• Connect an existing session to an OpenRig node

Build a custom fuzzer, a tool that tests code with many generated inputs, using LibAFL in Rust. Combine input mutation, execution feedback, scheduling, and target execution components when standard fuzzers offer insufficient control.

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• Build a fuzzer for a nonstandard target or architecture
• Implement custom input mutation and feedback strategies
• Prototype a new fuzzing research technique

Assess whether tests detect the wrong behavior relevant to a specific change, PR, or commit. Link findings to exact revisions, compare faulty and correct behavior when execution is authorized, and distinguish observed results from predictions.

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• Check whether a regression test detects the original bug
• Assess tests for a new feature
• Review behavior preservation during a refactor

Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.

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Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.

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Add and review preconditions on operations that delete, overwrite, rewrite history, or resolve a caller-supplied name to a filesystem path — refusing instead of warning, placing the guard ahead of the first mutation, structural classification rather than string-prefix matching, name validation plus resolved-path containment as two independent checks, why a guard on the destructive path is invisible to the dry-run, and mutation-testing each half separately. Use when writing or reviewing a `--rebuild`/`--reset`/`--purge` command, a bulk delete, a history rewrite, an `rm -rf`-shaped step, or any code that turns an argument into a file path.

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Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA/plasmid, AAV6), sizing homology arms, placing the cut within ~10 bp of the edit, and adding a mandatory codon-checked blocking (PAM/seed) mutation so the edited allele is not re-cut. Frames the HDR-vs-NHEJ-vs-MMEJ pathway competition, the MMEJ (PITCh) and homology-independent (HITI/HMEJ) alternatives for post-mitotic cells, ssODN strand/asymmetry choice, phosphorothioate end-protection, and ranked HDR enhancers. Use when designing a donor for a point mutation, epitope/fluorophore tag, allele replacement, or knock-in, or when HDR efficiency is low. Guide design and base/prime editing are separate skills.

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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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Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.

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Identify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstruction, focal vs broad/arm-level analysis, q-values from permutation) and quantify copy-number signatures with the Steele 2022 COSMIC framework and the Drews 2022 CINSignatures framework. Covers driver-gene localization from recurrence peaks, distinguishing focal drivers from arm-level passengers, and the caller-sensitivity caveats of copy-number signatures. Use when finding recurrently amplified or deleted regions in a cohort, localizing driver genes, separating focal from broad events, running GISTIC2, or extracting copy-number mutational signatures.

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EXPERIMENTAL — mutation testing with muter to measure whether tests actually assert anything: mutants that survive reveal assertion-free coverage. Advisory report only, never a merge gate. Use on engine/logic targets when coverage numbers look good but bugs still slip through.

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Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).

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Property-based testing strategies, mutation testing, shrinking, and combined PBT+mutation workflow for test quality validation

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Runs feature-scoped mutation testing to validate test suite quality. Use after implementation to verify tests catch real bugs (kill rate >= 80%).

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Operately test layout, naming (.projections.json), factories, feature/e2e steps, external query/mutation auth specs, and how to run Elixir/API/JS/EE tests. Use when adding, renaming, splitting, or reviewing tests; choosing where a test belongs; writing Factory/TurboCase/FeatureCase or ExternalApi QuerySpec/MutationSpec tests; or running make test / feature tests.

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Mutation testing ile test suite kalitesini olc. Stryker, mutmut, go-mutesting destegi.

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Assess tests for an identified code or test change, feature, PR or commit. USE FOR: review changed behavior or regression tests, prove pre-fix/missing behavior is detected, revision-bound red-green evidence. Polyglot. DO NOT USE without an identified change: hypothetical mutations or general suite blind spots (test-gap-analysis). Also exclude per-test readiness/A-F grades (grade-tests), coverage (coverage-analysis), new suites (code-testing), or mutation engines.

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Set up or refine open-source .NET code-quality gates for CI: formatting, `.editorconfig`, SDK analyzers, third-party analyzers, coverage, mutation testing, architecture tests, and security scanning. USE FOR: .NET quality gates in CI; analyzer, coverage, mutation, and architecture-test choices; standardizing `.editorconfig`, `dotnet format`, and warning policy. DO NOT USE FOR: non-.NET repositories; generic CI/CD guidance with no .NET quality stack decisions. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Use the open-source free `Stryker.NET` mutation testing tool for .NET. Use when a repo needs to measure whether tests actually catch faults, especially in critical libraries or domains. USE FOR: the repo uses or wants Stryker.NET; mutation testing is needed for high-risk code. DO NOT USE FOR: every PR path by default in a large repo; simple coverage collection. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Writes Convex queries, mutations, actions, and internal functions in the object form with args and returns validators, correct ctx usage, runtime boundaries, and error handling. Use when adding or changing anything in convex/*.ts that exports a function, or when deciding between query, mutation, and action.

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Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.

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Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".

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