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概要と使いどころ
Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome FASTA, quantifies in minutes. Outputs TPM/count tables (quant.sf) with optional GC- and sequence-bias correction. Integrates with tximeta/tximport for DESeq2/edgeR. Use STAR when a genome-aligned BAM is needed.
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Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.
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Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.
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Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR, NNT, Cohen's d), confounding, p-value vs clinical significance, GRADE quality assessment, reproducibility, and bias types (selection, information, confounding, reporting). Use when reading a paper or assessing claims.
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Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure filtering, Lipinski drug-likeness, reaction enumeration, 2D/3D coordinates. For simpler API use datamol; use RDKit for fine-grained sanitization, custom fingerprints, or SMARTS/reaction control.
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Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS, Golden Triangle, Ro3), structural alerts (PAINS, NIBR, Lilly Demerits), chemical group detectors, complexity metrics, and filter composition query language. Built on RDKit/datamol. For hit-to-lead filtering, library design, ADMET pre-screening. For molecular I/O use rdkit-cheminformatics or datamol.
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Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology (Planck18, distance/age), precise time (UTC/TAI/TT/TDB, Julian, barycentric), WCS pixel-world mapping, model fitting. For general tables use pandas/polars; for radio interferometry use CASA.
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Conducting systematic, scoping, and narrative literature reviews. Covers PRISMA/PRISMA-ScR protocols, search strategy (Boolean, MeSH), database selection (PubMed, Scopus, Web of Science, Embase), screening, data extraction, evidence synthesis (narrative, meta-analysis, thematic), and reporting. Use when planning or executing a formal literature review.
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Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.
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Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric ops (buffer, simplify, centroid, affine), spatial analysis (joins, overlays, dissolve, clipping, distance), visualization (choropleth, interactive maps, basemaps). Use for spatial joins, overlays, CRS transforms, area/distance, maps.
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Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
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Statistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions (histplot, kdeplot), categorical (boxplot, violinplot), relational (scatterplot, lineplot), regression (regplot, lmplot), matrix (heatmap, clustermap), grids (pairplot, FacetGrid). Use for quick statistical summaries; matplotlib for fine control; plotly for interactive HTML.
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Drive a PR to an approved code review by looping OCR's multi-agent review and address steps. Runs /ocr:review then /ocr:address repeatedly until the review verdict is APPROVE, then one final /ocr:address for leftover suggestions, posting every review and every address round to the GitHub PR as comments. Use when the user asks to 'review and address in a loop', 'iterate review until approved', 'auto review-and-fix this PR', 'loop /ocr:review and /ocr:address', or to take a changeset all the way to a clean APPROVE with the default reviewer team. Wraps the /ocr:review (.ocr/commands/review.md) and /ocr:address (.ocr/commands/address.md) skills; needs a feature branch with an open GitHub PR and the gh CLI for posting.
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Patterns and best practices for integrating ROS2 systems with web technologies including REST APIs, WebSocket bridges, and browser-based robot interfaces. Use this skill when building web dashboards for robots, streaming camera feeds to browsers, exposing ROS2 services as REST endpoints, or implementing bidirectional WebSocket communication between web UIs and ROS2 nodes. Trigger whenever the user mentions rosbridge, rosbridge_suite, roslibjs, FastAPI with ROS2, Flask with rclpy, WebSocket for robot telemetry, MJPEG streaming, WebRTC for robots, REST API wrapping ROS2 services, web-based robot control, browser robot interface, robot dashboard, CORS configuration for robots, or any web-to-ROS2 bridge pattern. Also trigger for authentication on robot web interfaces, rate limiting sensor streams, video streaming from robot cameras to browsers, or running async web frameworks alongside the ROS2 executor. Covers rosbridge_suite, FastAPI, Flask, WebSocket, and WebRTC approaches.
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Comprehensive guidance for building web apps with opinionated defaults for tech stack, design system, and code standards. Use when user wants to create a new web application, dashboard, or interactive interface. Provides tech choices, styling guidance, project structure, and design philosophy to get users up and running quickly with a fully functional, beautiful web app.
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Direct, build and render premium cinematic motion design from code — launch films, product and feature videos, looping feature animations for landing pages and social, logo stings and reveals, UI walkthroughs, app demos, kinetic type, teasers, trailers, intros and promo clips. Use this whenever the user wants any video, animation, motion graphic or animated demo made with Remotion, HyperFrames, HTML/GSAP or React, or asks to storyboard, time, score, render, polish or critique one — even if they only say "make a video about X", "animate this feature" or "we need a launch clip". It supplies concept and copy discipline, type and colour taste that defers to a supplied brand, a beat-locked timeline that drives both picture and a code-made soundtrack, choreography and transition craft, real product UI in motion, film-grade finishing (true motion blur, no banding, BT.709, sync-checked mux) and a measured self-critique loop on contact sheets and renders.
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Turn Chinese classical poems and ci into coherent vertical Chinese-art videos with poem-driven scene grouping, GPT ImageGen stills, Docker-only Gemini I2V, retained model-generated ambience, Gemini sparkle-watermark cleanup, brush-calligraphy captions revealed character by character, optional local BGM mixing, stitching, and final-frame QA. Supports verse-driven variation across ink landscape, gongbi bird-and-flower, colored figure-and-horse painting, blue-green landscape, xuan paper, silk, and related Chinese visual languages. Use when users ask for 古诗词动态视频、诗词逐句或两句一景、国风视频、毛笔字逐字出现、整首诗拼接成片，or want the established 月落乌啼霜满天 workflow applied to another poem.
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SST v4 (Ion) expert for managing AWS resources as code with the Pulumi-backed framework. Use when writing or editing sst.config.ts, building infra/ modules (sst.aws.Function/Bucket/Dynamo/Cron/Service/Router, sst.Secret, sst.Linkable, raw aws.* Pulumi resources), wiring resource links, scoping IAM, or running sst deploy/dev/diff/remove. Essential when the user mentions SST, sst.config.ts, $config, $transform, $interpolate, sst.aws.*, sst.Secret, Pulumi/Ion, "sst deploy", a failed SST deploy (ConflictException on a resource-type change, "Identifier '__filename' has already been declared", MalformedPolicyDocument on an Output<T>), or wants to scaffold/troubleshoot AWS infrastructure with SST. Also use when a request to "deploy my AWS stack" or "add a Lambda/bucket/table" is made in a repo that already contains an sst.config.ts (using $config) or an sst dependency. Do NOT use when the task is primarily AWS CDK, Terraform, raw CloudFormation, or SAM with no SST present — those have their own tooling.
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Provides AWS CloudFormation patterns for Amazon S3. Use when creating S3 buckets, policies, versioning, lifecycle rules, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.
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Provides AWS CloudFormation patterns for CloudWatch monitoring, metrics, alarms, dashboards, logs, and observability. Use when creating CloudWatch metrics, alarms, dashboards, log groups, log subscriptions, anomaly detection, synthesized canaries, Application Signals, and implementing template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references, and CloudWatch best practices for monitoring production infrastructure.
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Provides AWS CloudFormation patterns for Amazon RDS databases. Use when creating RDS instances (MySQL, PostgreSQL, Aurora), DB clusters, multi-AZ deployments, parameter groups, subnet groups, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.
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Provides AWS CloudFormation patterns for DynamoDB tables, GSIs, LSIs, auto-scaling, and streams. Use when creating DynamoDB tables with CloudFormation, configuring primary keys, local/global secondary indexes, capacity modes (on-demand/provisioned), point-in-time recovery, encryption, TTL, and implementing template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references.
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Provides AWS CloudFormation patterns for EC2 instances, Security Groups, IAM roles, and load balancers. Use when creating EC2 instances, SPOT instances, Security Groups, IAM roles for EC2, Application Load Balancers (ALB), Target Groups, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.
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Provides patterns for unit testing JSON serialization/deserialization with Jackson and `@JsonTest`. Validates JSON mapping, custom serializers, date formats, and polymorphic types. Use when testing JSON serialization, validating custom serializers, or writing JSON unit tests in Spring Boot applications.
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。