「sem」の検索結果

Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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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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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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Interactive Archon integration for knowledge base and project management via REST API. On first use, asks for Archon host URL. Use when searching documentation, managing projects/tasks, or querying indexed knowledge. Provides RAG-powered semantic search, website crawling, document upload, hierarchical project/task management, and document versioning. Always try Archon first for external documentation and knowledge retrieval before using other sources.

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Decide whether commonly-excluded patients (eating disorders, elderly ≥75, upper GI disease) can actually receive a GLP-1 receptor agonist. Use when a clinician asks "can I give semaglutide to a patient with binge eating disorder / anorexia / bulimia", "is liraglutide safe in an 80-year-old", "GLP-1 with GERD or chronic gastritis", "GLP-1 in sarcopenic elderly", or anytime a patient is being ruled out for GLP-1 therapy based on a perceived contraindication. Grounded in Gorgojo-Martínez 2023 §6 (Myths or Reality).

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Select the right pharmacologic agent for a child aged 12+ with obesity using the CMAJ 2025 guideline — choosing between GLP-1 receptor agonists, metformin, or orlistat with monitoring guidance. Trigger when a clinician asks which medication to use for pediatric obesity, whether to start semaglutide or metformin in a child, or how to manage obesity pharmacologically in adolescents.

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Reconcile baseline-versioned files that the `create-baseline upgrade` CLI staged for LLM-assisted semantic merge. Use when the CLI prints "Open Claude Code and run /upgrade-project to reconcile". Reads the stage manifest at `.claude/state/upgrade/<ts>/manifest.json`, reasons through each pending file's three-way delta in main context, writes a reconciled LOCAL, then deletes the stage when every file lands. Supports `--dry-run` (preview the reconciled diff without writing) and a structured "needs-user-input" fallback when the conflict cannot be disambiguated automatically.

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Read-only release + backlog recap. Reports the last release, commits-since-tag classified by conventional-commit type with the semver bump they trigger and pushed-vs-origin state, the backlog bucketed (open/picked-up/dropped with epic parent→child nesting), the roadmap epics with their per-task tallies, and condensed open questions — then recommends the next pickup. One `cli.mjs recap` call returns all six recap keys. Invoke any time (on demand) to plan a release or choose the next thing to build; a compact form is also surfaced at session start. Not a workflow phase; never writes CHANGELOG; never starts or commits work.

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On-demand "what's new" generator. Main context (which knows the impending change) writes keepachangelog-style entries to a fragment file at `.claude/state/whatsnew/<slug>.json` (gitignored, transient). An optional per-project `project.json → whatsnew.route_workflow` names a routing workflow that consumes the fragment and renders it wherever the project wants (a site page, a release body, a docs page). Not a workflow phase — it never blocks a commit, and it never writes `CHANGELOG.md` (that file is owned solely by semantic-release in CI).

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Find web sources with query-relevant page excerpts and optional full-page content, and discover workflows, data APIs, and indexes. Use for web research or finding structured records, listings, transcripts, and datasets. Supports semantic tool discovery, domain matching, and progressive catalogue browsing.

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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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Pure API reference for reddapi.dev - authentication, all endpoints (vector search, semantic search, trends, subreddit lookup), request parameters, response schemas, and error codes, with no research-workflow framing. Use when the user wants raw endpoint documentation, is debugging a reddapi.dev integration, needs exact request/response field names, or asks for 'reddapi API reference', 'reddapi.dev endpoints', or 'reddapi error codes'. For guided research workflows and query playbooks, see reddit-research. For B2B lead scoring, see reddit-leads.

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Do market research, user research, and product validation on Reddit with semantic search across 50K+ subreddits, 20M+ posts, and 40M+ comments via reddapi.dev - search by meaning, not keywords, no Reddit OAuth or app registration needed. Use when the user wants to research what people say on Reddit, find user pain points and complaints, validate a product or niche idea, do competitor and market research, track subreddit trends over a date range, or discover which subreddits discuss a topic. Also use when the user mentions 'Reddit research', 'Reddit 调研', 'search Reddit', 'subreddit discovery', 'niche validation', 'pain points', 'user complaints', or 'Reddit trends'. Requires REDDAPI_API_KEY. For B2B lead scoring, see reddit-leads; for a bare API reference, see reddit-search-api.

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Shape an article as a journey of beats, choose-your-own-adventure style. The user picks a starting beat from the raw material, you write only that beat, then offer options for where to pivot next, beat by beat, until the article reaches a natural end. Use when the user has raw material and wants to assemble it as a narrative rather than an argument.

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Prepare and risk-check the next rolling-wave slice for implementation. Use when the user wants to continue a rolling-wave project, draft one bounded slice in the main context by default, use a fresh planning author only when context or discovery cost warrants it, use a fresh preparation reviewer when semantic risk or uncertainty warrants independent pressure-testing, decompose parallel implementation chunks where appropriate, identify agent, human, either, or hybrid execution fit, write or update docs/rolling-wave/{project}/slices/NNN-slug.md, and mark that slice ready even when other slices are active.

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Bump the package version and create an annotated git tag. Accepts a semantic version number (1.2.0) or a bump type (patch, minor, major). Does not push — use the publish skill to push. Use as part of a release workflow.

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Expert-level nanotechnology covering nanomaterials, nanofabrication, characterization methods, nanoelectronics, nanomedicine, and self-assembly.

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Expert-level compiler design covering lexical analysis, parsing, semantic analysis, intermediate representations, optimization passes, and code generation.

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Bun runtime, package manager, bundler, and test runner. Use when running scripts with bun, managing packages, serving HTTP with Bun.serve, querying databases with Bun.sql/bun:sqlite/Bun.redis, shell scripting with $, using S3/file I/O, writing tests with bun:test, bundling or compiling to executable, or using any Bun-specific API (spawn, glob, semver, FFI, workers, plugins, HTMLRewriter).

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Jev (TypeSafe System One) inner loop for ego-browser — one ~0.4 s typed decision per DOM step instead of an LLM turn. Use for multi-step clicking through a semantic page: fill known values into a form, set filters, open a row/card/menu by name, reach a page via nav or site search. Escalates login, payment, free text, canvas and content reading back to you.

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Design and review intuitive, scalable, maintainable HTTP APIs. Use this skill whenever the user wants to design a new REST API, review an existing API or spec, write OpenAPI 3.x definitions, or work with HTTP semantics (GET/POST/PUT/PATCH/DELETE), status codes, idempotency (Idempotency-Key), error envelopes (RFC 7807 problem+json), pagination, filtering, versioning, or API auth (API keys, OAuth2 client credentials, rate limits). Also trigger for "API design", "RESTful", "endpoints", "OpenAPI", "Swagger", "ReDoc", "contract testing", or GraphQL and gRPC design questions.

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Audit datasets, joins, labels, and ground truth before analysis or modeling. Use when data meaning, row grain, time semantics, source-of-truth reliability, or label construction may invalidate conclusions; not for general model evaluation after the evidence base is already trusted.

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Govern the SemVer release process — versioning discipline, tag-based GitHub releases, changelog hygiene, and the ADR that confirms the release strategy is agreed. Trigger when setting up a release process, before a first public release, or when release practice has become inconsistent. Owned by delivery-orchestrator.

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。