「ker」の検索結果

End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.

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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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Biological knowledge: query curated assertions and reference databases for genes, variants, pathways, regulation, cell types, reference atlases, perturbation-derived relationships, phenotypes, therapeutic targets, drugs, interactions, annotations, signatures, compounds, and predicted structures. Use for identifiers, marker sets, gene sets, associations, ontologies, database facts, and cross-database coverage.

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Experimental data: discover and acquire raw or near-raw measurements, sample-level observations, and reusable datasets from sequencing, transcriptomics, single-cell, perturbation, proteomics, metabolomics, genomics, and structural-biology repositories. Use for study or sample metadata, matrices, reads, spectra, experimental structures, and downloadable research artifacts—not curated database assertions or reference marker collections.

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Decision-grade statistical analysis for metabolomics intensity tables. Covers transformation and scaling (Pareto vs unit-variance as a hidden hypothesis), unsupervised structure (PCA/HCA for QC), permutation-validated PLS-DA/OPLS-DA (R2 vs Q2, double CV, VIP as heuristic), univariate testing (Welch/Mann-Whitney/ANOVA/LMM with covariate adjustment), and dependence-aware multiple testing. Use when testing which metabolites differ, building or validating a discriminant model, choosing a scaling, or correcting many correlated tests. For sample-wise normalization/drift correction see metabolomics/normalization-qc; for ML classifiers and selection-inside-CV leakage see machine-learning/biomarker-discovery and machine-learning/model-validation; for pathway interpretation see metabolomics/pathway-mapping; for design/power/multiplicity regime see experimental-design/multiple-testing.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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JTBD (Jobs to Be Done) v3.0 完整工具集。融合四大学派--Klement 进步力量、 Ulwick ODI 机会算法、Wunker Jobs Atlas 七维度、Kalbach Job Stories 整合-- 提供 13 项可执行能力和 15 篇方法论知识库。附带完整 Python API(JTBDSkill 统一入口), 覆盖访谈→问卷→评分→优先级→竞争→营销→增长→描述→Job Map→Outcome→Stories→障碍→Atlas 全流程,以及 CEO 决策视角的市场规模估算、优先级评分与商业化可行性分析。

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Simulate the SCF team's manual prescreen on a Build Award submission — a completeness and eligibility check applied to every full submission before panel review. Checks completeness, Stellar integration, eligibility, budget issues, and common disqualifiers. Use when reviewing a draft Build Award submission for readiness before it goes to the SCF round.

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Prove repository ownership, module ownership, assembly boundaries, edit-marker rules, extension points, and test placement.

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Extract structured data from multiple invoice PDFs in one call, then pipe the results directly into an XLSX accounts payable tracker.

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Extract line-level charges from multiple carrier invoices, then generate an XLSX freight cost tracker in a single pipeline.

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Imports a custom RoadRunner map (FBX geometry + XODR OpenDRIVE) into a CARLA source build as a drivable map — reads the map from the directory the user names, runs CARLA's Import.py to cook the level, Traffic Manager graph and (standard maps only) pedestrian navmesh, and verifies it loads on a server. Handles both standard maps and large tiled maps; large maps get no navmesh, matching upstream CARLA. Use when the user asks to "import a map into CARLA", "add a custom/RoadRunner map", "ingest an FBX+XODR map", "make import", bring in a "large/tiled map", or fix missing walkers / a missing pedestrian navmesh.

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Visualises and validates a map's pedestrian navigation mesh by sampling walkable locations (get_random_location_from_navigation) and drawing them as debug points. Use when the user asks to "show/visualise the pedestrian navmesh", "check walkable areas", "validate pedestrian navigation after a map import", or "why won't my walkers move". Confirms the navmesh loaded and how far it covers.

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Downloads CARLA so nothing has to be fetched by hand — an official release package for any published version (resolved live from the GitHub releases, with AdditionalMaps), the rolling nightly Dev build, a shallow source checkout of a branch or tag, or the carlasim/carla Docker image. Reports exactly what was obtained and where, plus the environment variables the other skills read. Use when the user asks to "download CARLA", "get CARLA 0.9.16", "install CARLA", "clone the carla repo", "fetch the latest CARLA", or has no CARLA at all yet.

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Inspects and visualises a ROS-2-enabled CARLA server from Docker containers, with no local ROS 2 install — list/echo/rate-check topics (the "are the topics actually on the wire" check), run the bundled map-and-lidar demo stack (hero vehicle with camera/lidar/GNSS/IMU on autopilot), and open RViz2 with the lane-network preset. Use when the user asks to "check the ROS topics", "echo /carla/map", "is CARLA publishing to ROS", "visualise the lidar in RViz", "open rviz", or "run the ROS 2 demo".

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Adds a new ROS 2 message type to CARLA's native ROS 2 interface — the hand-written POD struct under LibCarla/source/carla/ros2/types/msg, its Fast-CDR serialize/deserialize pair, the RIHS01 type hash computed in Docker, the CdrTopicInfo registration and the type-hash test. Use when the user asks to "add a ROS message type", "support sensor_msgs/X in CARLA", "add a carla_msgs type", "why is my type hash warning appearing", or needs a message CARLA does not publish yet. There is no IDL codegen — every step is manual.

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Autonomous DevSecOps & FinOps Guardrails. Orchestrates Gemini 3 Flash to audit Linux Kernel patches, Terraform cost drifts, and K8s compliance.

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Multi-agent debate orchestration for Architecture Decision Records. Automatically triggers on ADR create/edit/delete. Coordinates architect, critic, independent-thinker, security, analyst, and high-level-advisor agents in structured debate rounds until consensus.

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Provide comprehensive techniques for attacking Microsoft Active Directory environments. Covers reconnaissance, credential harvesting, Kerberos attacks, lateral movement, privilege escalation, and domain dominance for red team operations and penetration testing.

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ADA accessibility compliance checking skill for routes, slopes, and pedestrian facilities

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Discover and configure Bluetooth and Wi-Fi accessories using AccessorySetupKit. Use when presenting a privacy-preserving accessory picker, defining discovery descriptors for BLE or Wi-Fi devices, handling accessory session events, migrating from CoreBluetooth permission-based scanning, or setting up accessories without requiring broad Bluetooth permissions.

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Ensures designs meet accessibility requirements including WCAG compliance, color contrast, keyboard navigation, screen reader support, and focus management. Reviews designs for accessibility issues and provides recommendations.

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Use when working with access policies, field access, authorization middleware, gates, route access control, AccessResult semantics, permission handlers, or files in packages/access/, packages/routing/src/AccessChecker.php, packages/user/src/Middleware/. Covers entity-level access (deny-by-default via isAllowed), field-level access (open-by-default via !isForbidden), the Gate system, route options (_public, _permission, _role, _gate), and the SessionMiddleware/AuthorizationMiddleware pipeline in public/index.php.

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Accessibility audit for CSS covering focus styles, color contrast, text sizing, screen reader support, and WCAG compliance. Provides actionable fixes. Use when auditing accessibility or fixing a11y issues.

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