「ept」の検索結果

End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/beta diversity at a declared sampling depth (phyloseq/vegan, adonis2 paired with betadisper), compositional DA as a consensus of >=2 tools (ALDEx2/ANCOM-BC2) on unrarefied counts, and optional PICRUSt2 functional prediction gated on NSTI. Covers the stage-ordering decisions (primers before truncation, per-run error model, rarefy for diversity not DA, predicted potential not activity) and defers each per-step choice to the six microbiome skills. Use when staging an amplicon study end to end or chaining ASV inference, taxonomy, diversity, and differential abundance. For shotgun reads see workflows/metagenomics-pipeline.

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Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance + IP-enrichment QC, PreSeq saturation curves, exomePeak2 (transcript-aware Poisson GLM) peak calling, optional MACS3 broad-peak cross-check, DRACH motif confirmation as a sanity check (NOT a per-peak filter), exomePeak2 differential calling via the four-BAM-vector interface (bam_ip + bam_input control; bam_treated_ip + bam_treated_input treatment), ChIPseeker annotation, and the canonical Guitar metagene with stop-codon enrichment as the biological QC anchor. Use when running a complete MeRIP analysis from raw reads, when chaining the constituent epitranscriptomics skills (merip-preprocessing -> m6a-peak-calling -> m6a-differential -> modification-visualization), or when wrapping the pipeline in Snakemake / Nextflow.

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TOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in ToolUniverse docs. Wrong code, broken links, incorrect counts, and overlapping instructions must be fixed or removed — never left in place. Runs five phases: (D) static method scan, (C) live code execution, (A) automated validation, (B) ToolUniverse audit, (E) less-is-more simplification. Core philosophy: each concept appears exactly once; remove don't add; no emojis; single setup entry point. Use when reviewing docs, before releases, after API changes, or when asked to audit, fix, or simplify documentation.

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Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.

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Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3 with constraints), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.

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Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mummichog/PSEA on raw m/z peaks, and network-diffusion enrichment (FELLA), with correct background-set construction and honest interpretive ceilings. Use when interpreting differential metabolites or an untargeted LC-MS feature table in pathway context, choosing ORA vs MSEA vs mummichog vs topology, or setting the reference/background set. For annotation confidence levels feeding ORA see metabolomics/metabolite-annotation; for gene-set concepts see pathway-analysis/go-enrichment and pathway-analysis/gsea; for joint gene+metabolite pathways see multi-omics-integration/mofa-integration.

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Use to process automated PR review feedback (Copilot, Greptile, Codex) and iterate until all AI threads are addressed, checks are green, and the PR is merge-ready. Trigger when the user says "address review feedback", "recycle reviews", or references an automated reviewer.

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Use every time you push a commit to an active pull request, to verify the PR is truly stable before reporting merge readiness. Covers the post-push wait window, AI review audit (Copilot/Greptile/Codex), and the gh commands to snapshot PR state. Trigger on "I pushed" or "is the PR ready to merge".

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Review code changes adversarially using parallel review layers (Blind Hunter, Edge Case Hunter, Acceptance Auditor) with structured triage into actionable categories. Use when the user says "run code review" or "review this code"

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Working Backwards PRFAQ challenge to forge product concepts. Use when the user requests to 'create a PRFAQ', 'work backwards', or 'run the PRFAQ challenge'.

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Apple's approach to interface design and fluid, physical motion, translated for the web. Use when building or reviewing gesture-driven UI, spring animations, drag/swipe/sheet interactions, momentum and interruptible transitions, translucent materials and depth, typography (optical sizing, tracking, leading), reduced-motion, or the design foundations (feedback, spatial consistency, restraint) behind Apple-style interfaces.

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Turn product requirements into scoped tasks with dependencies and acceptance criteria. Use for implementation planning and prioritization.

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Design proof-of-concept frameworks for AI projects. TRIGGERS - Use when user needs help with ai-poc-framework related tasks.

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Extract proof-of-delivery number, recipient, delivery time, items, exceptions, and signature status from delivery receipts.

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Listens to a CARLA sensor and either saves its data to files, shows it live in a window, prints a one-shot summary, or (ros-info) reports the native ROS 2 topics, QoS and enabled-for-ROS state so you can echo it from ROS instead. Cameras save as PNG (depth/semantic auto-colourised) and display in a pygame window; lidar saves as .ply and shows as a top-down scatter; IMU/GNSS/radar/collision stream to JSONL or the console. Use when the user asks to "show/view the camera", "display the lidar", "save the sensor data / capture a dataset", or "what is this sensor reading". Select the sensor by id, type, or the actor it's attached to.

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SQLite-based ticket tracking for structured development workflows. Use this skill when the user asks to initialize a ticket database, import requirements, list tickets, get the next ticket to work on, mark tickets as done, or check ticket status. Essential for managing epics, user stories, and acceptance criteria.

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MUST USE for building FastAPI/REST API applications with Aerospike database (aerospike-py Rust/PyO3 async client). Covers AsyncClient lifespan management, FastAPI Depends injection, aerospike_py exception-to-HTTP-status mapping (RecordNotFound→404, RecordExistsError→409, BackpressureError→503, AerospikeTimeoutError→504), POLICY_EXISTS_CREATE_ONLY/UPDATE_ONLY for CRUD semantics, NamedTuple attribute access (record.bins not tuple unpacking), client.ping() readiness probe, batch_read returning dict, batch_write with in_doubt retry signal, and global AerospikeError handler. Triggers on: FastAPI + Aerospike, REST API + aerospike-py, CRUD API with Aerospike, client.ping() health probe, batch_read/batch_write endpoint, web server/HTTP service backed by Aerospike NoSQL, uvicorn + Aerospike.

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Use when you need to design, review, or improve security in Quarkus applications — including Quarkus Security with JWT/OIDC, basic auth, @RolesAllowed / @Authenticated / @PermitAll, SecurityIdentity, permission checks, path-based authorization in configuration, exception mapping for auth failures, and sensitive-data-safe logging. This should trigger for requests such as Add Quarkus security support; Review Quarkus security configuration; Improve API authorization in Quarkus; Add JWT/OIDC security in Quarkus; Harden Quarkus authorization rules. Part of cursor-rules-java project

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Use when you need to design, review, or improve security in Micronaut applications — including micronaut-security authentication, @Secured and intercept-url-map rules, JWT/session strategies, SecurityService checks, CORS, CSRF awareness for browser apps, rejection handlers, and sensitive-data-safe logging. This should trigger for requests such as Add Micronaut security support; Review Micronaut security configuration; Improve API authorization in Micronaut; Add JWT security in Micronaut; Harden Micronaut route authorization rules. Part of cursor-rules-java project

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PHP Standards Recommendations (PSR) overview knowledge base. Provides comprehensive reference for all accepted PSRs including PSR-1,3,4,6,7,11,12,13,14,15,16,17,18,20. Use for PSR selection decisions and compliance audits.

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