「can」の検索結果

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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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Advanced vulnerability analysis principles. OWASP Top 10 baseline + current threat landscape awareness, Supply Chain Security, attack surface mapping, risk prioritization. Use when performing security audits, threat modeling, or OWASP reviews. NOT for STRIDE/CSO-mode infrastructure audits (see mk:cso).

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Chief Security Officer mode. Infrastructure-first security audit: secrets archaeology, dependency supply chain, CI/CD pipeline security, LLM/AI security, skill supply chain scanning, plus OWASP Top 10, STRIDE threat modeling, and active verification. Two modes: daily (zero-noise, 8/10 confidence gate) and comprehensive (monthly deep scan, 2/10 bar). Trend tracking across audit runs. Use when: "security audit", "threat model", "pentest review", "OWASP", "CSO review".

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Experimental/manual harness canary procedure. It records benchmark manifests and scores but does not provide a fully automated runner.

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Use when taking a repo open source, or hardening one that already is. Run /oss-launch and it scans the repo (stack, existing files, git remote, secrets), asks only what it cannot infer, then generates a tailored OSS file collection (README, LICENSE, CONTRIBUTING, CODE_OF_CONDUCT, SECURITY, CHANGELOG, .gitignore, .github/ issue + PR templates, CI/CD). Also covers launch (GitHub metadata, badges, Show HN, Reddit, YouTube), release cadence (SemVer + CHANGELOG), and demo-GIF generation. Triggers on "open source this", "OSS checklist", "prep for launch", "make this repo public", "add a license / contributing / security policy", "Show HN", "release workflow", "star growth", "get contributors".

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Find UX pains and opportunities fast through competitor scans, pattern research, and web search. Surfaces how others solve the same flow, common failure modes, and conventions users already expect. Use when the user says "research this UX", "how do others do X", "competitor scan", "find UX patterns", "what's the convention for Y", or before ideating a flow. Part of the Product Design set. Uses web search/fetch tools.

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Walks a cardiologist through whether, where and how to order a germline genetic test for a suspected inherited cardiovascular disease: indication, written consent (with assent for minors), pre-test counseling, choice of test and laboratory, handling of VUS and secondary findings, and privacy. Use when a clinician asks 'should I order a genetic test', 'how do I consent for a cardiomyopathy or long QT gene panel', 'can I test this child or relative (cascade screening)', 'what do I tell the patient about VUS or a negative result', or 'where can this test be sent'. Based on the JCS/JCC/JSPCCS 2024 guideline; Japan-specific insurance and legal details are flagged.

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Assess whether a hospitalized adult with diabetes on insulin pump therapy remains a candidate for continued inpatient pump use. Consider triggers such as the clinician asking "Is this patient appropriate to continue insulin pump in hospital?" and evaluate for impaired consciousness, inability to adjust pump settings, critical illness, DKA, or hyperosmolar hyperglycemic state.

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Applies standard breast-screening guidelines for transgender females who have been assessed as having no known increased risk of breast cancer. Trigger phrases include transgender female and assessed as no increased breast cancer risk.

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This skill determines whether testicular volume should be used as the primary or sole indicator of sexual development in male childhood cancer survivors who have received gonadotoxic treatments such as alkylating agents or testicular radiotherapy. Triggers include clinician questions like “Can I use testicular volume to assess puberty in this male survivor after chemotherapy?” or “Is testis size reliable for sexual maturity evaluation post‑radiation?”

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This skill determines whether a patient using a hybrid closed-loop insulin pump can continue this therapy upon hospital admission. It is triggered by questions such as "Can hybrid closed-loop pump be continued given hospital constraints?"

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Dev-only check that a drafted spec for THIS baseline repo won't ship dev-tree references to consumer installs. Catches three failure modes — shipped SKILL.md prose that references paths under `src/`, `tests/`, `scripts/`, `obj/` as runtime invocations (in ```bash fences``` OR `inline backticks`, plus shipped `.mjs`/`.js`/`.sh`/`.py` helper-file imports); new Python helpers added under `.claude/skills/<slug>/` (shipped helpers must be `.sh` or `.mjs`/`.js` going forward); and imports of modules that aren't in `obj/template/.claude/manifest.json` (consumer won't have the file). The aggregate scanner (`scan-shipped-skills.mjs`) walks only baseline-owned skill dirs (via `owner: baseline` frontmatter) at top level — `references/` and other subdirs are documentation, not runtime. BLOCKER findings hard-block implementation entry; ADVISORY surfaces but doesn't block. Read-only — surfaces a punch list; maintainer edits the spec and re-runs until CLEAN.

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Workflow Phase 3 — Research and Solution Exploration. Surfaces 2–4 candidate solution approaches with concrete tradeoffs, grounded in current library docs (fetched through the provider named in `.claude/docs-provider.json`) — never in training-data recall. Output lives at `docs/research/<slug>.md`. Candidate ranking and the memo execute in main context; doc/source gathering MAY be delegated to read-only advisory subagents (seed.md §4.2-A).

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Canvas API Connection Skill

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Builds the "Report Sources" child page for a finished Weekly Community Signal report — an evidence-backed defense of WHY every item landed in the column/section/rank it did. The agent argues each placement like a lawyer (claim → evidence → rule → rebuttal) but is under oath: it CANNOT invent, spin, or overstate — every claim ties to a verifiable fact (issue #, label, PR type, quoted comment, npm output, the front-door test). Not CYA — it's so Nathan can defend the report with facts and see the exact reasoning behind each call. Runs after the report (invoked by weekly-report, last steps) and on "report sources", "defend the report", "why is this here".

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Subagent that scans CopilotKit + AG-UI releases shipped in (and just after) the report window, diffs the git tags to extract what each release actually fixed, and returns a fix-map the weekly-report writer cross-checks against open issues. Catches issues that are quietly already-fixed in a shipped release, and is the authoritative source for the "current release vX.Y.Z" version claims. Invoked by weekly-report (spawned in parallel with the Discord/GitHub pulls); runs as a general-purpose subagent so the orchestrator's context stays small.

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If you can imagine it, CellCog can film.

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Cancel a running Claude Companion job.

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Scan the codebase for common security issues: hardcoded secrets, SQL injection vectors, XSS, unvalidated inputs, and insecure defaults. Use before deploying, as part of code quality review, or when asked to check for security issues.

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Use when designing engineering 1:1s — cadence, agenda mix, growth-vs-blocker-vs-trust shape, cancellation anti-patterns. Triggers on 'fix my 1:1s', 'should I cancel 1:1s this week'.

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