1.3K skills · sorted by relevance
Coordinate specialized AI agents to develop research hypotheses, plan methods, run computational experiments, search literature, and draft journal-formatted LaTeX papers. Start from a dataset description or supply existing ideas, methods, and results at individual stages.
Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.
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Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to
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Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stoc
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Use when you need to write fast unit tests for Quarkus applications — including pure tests with @ExtendWith(MockitoExtension.class), @QuarkusTest with @InjectMock for full CDI mock replacement, @InjectSpy for partial CDI bean mocking, REST Assured for resource-focused tests, @ParameterizedTest with @CsvSource / @MethodSource, QuarkusTestProfile for test-specific configuration overrides, and naming conventions (*Test → Surefire, *IT → Failsafe). For framework-agnostic Java use @131-java-testing-unit-testing. This should trigger for requests such as Add or improve unit tests in a Quarkus project; Reduce slow @QuarkusTest usage with Mockito-first tests; Add @InjectSpy partial mocking or QuarkusTestProfile configuration in Quarkus tests; Convert repeated test methods to @ParameterizedTest with @CsvSource or @MethodSource; Write fast pure unit tests for Quarkus services. Part of Plinth Toolkit
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Provides patterns for testing utility classes, static methods, and helper functions. Validates pure functions, null handling, edge cases, and boundary conditions. Generates AssertJ assertions and @ParameterizedTest for string utils, math utils, validators, and collection helpers. Use when testing utils, test helpers, helper functions, static methods, or verifying utility code correctness.
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Think and work like an expert Formal Methods Researcher. Use when a task calls for Formal Methods Researcher judgment. Reasons from operational semantics and temporal logics through SPIN/TLA+/PRISM, Coq/Lean/Isabelle, Z3/CVC5, refinement and separation logic, vacuity and false-positive diagnosis, and Dafny/F* versus property-based testing boundaries.
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AI 短剧 (AI 微短剧) (AI 短剧 (AI 微短剧) (从业者视角) — 用 AIGC 工具（AI 视频生成 / AI 脚本 / AI 生图 / AI 配音 / 对口型 / 角色一致性）制作竖屏微短剧并变现的新兴行业。覆盖: (a) 创作工作流 — 选题→剧本/分镜→AI 生图→图生视频(首尾帧/运镜/参考)→配音/对口型→剪辑/调色→成片，其中角色/场景一致性是第一性难题; (b) 工具栈 — 视频生成(可灵 Kling / 即梦 Seedance / 海螺 Hailuo / Vidu / Runway Gen / OpenAI Sora / Pika / Luma / Pixverse)、脚本(LLM)、生图(Midjourney/SD/即梦)、配音(TTS)、对口型、剪辑(剪映/CapCut); (c) 商业/变现 — 国内付费投流(IAP + ROI + 平台分账, 抖音/快手/红果/微信小程序短剧)与海外订阅(ReelShort/DramaBox/ShortMax/GoodShort)两套打法、品牌定制、成本结构; (d) 合规 — 中国《人工智能生成合成内容标识办法》(2025-09 强制 AI 标识)、广电微短剧备案与分类分层审核、版权与肖像权。主战场 = 抖音/快手/视频号/B站 + 海外短剧 App。学派分歧: 纯 AI vs AI+实拍混合、国内投流 vs 海外订阅、视频工具派之争、「AI 短剧是真需求还是伪风口」。不含: 传统实拍短剧制作、通用影视编剧(已有 scriptwriting skill)、短视频信息流投放(已有 short-video-ads skill)、纯 AI 视频底层技术研发。) Master OS — automated mastery of AI 短剧 (AI 微短剧) (从业者视角) — 用 AIGC 工具（AI 视频生成 / AI 脚本 / AI 生图 / AI 配音 / 对口型 / 角色一致性）制作竖屏微短剧并变现的新兴行业。覆盖: (a) 创作工作流 — 选题→剧本/分镜→AI 生图→图生视频(首尾帧/运镜/参考)→配音/对口型→剪辑/调色→成片，其中角色/场景一致性是第一性难题; (b) 工具栈 — 视频生成(可灵 Kling / 即梦 Seedance / 海螺 Hailuo / Vidu / Runway Gen / OpenAI Sora / Pika / Luma / Pixverse)、脚本(LLM)、生图(Midjourney/SD/即梦)、配音(TTS)、对口型、剪辑(剪映/CapCut); (c) 商业/变现 — 国内付费投流(IAP + ROI + 平台分账, 抖音/快手/红果/微信小程序短剧)与海外订阅(ReelShort/DramaBox/ShortMax/GoodShort)两套打法、品牌定制、成本结构; (d) 合规 — 中国《人工智能生成合成内容标识办法》(2025-09 强制 AI 标识)、广电微短剧备案与分类分层审核、版权与肖像权。主战场 = 抖音/快手/视频号/B站 + 海外短剧 App。学派分歧: 纯 AI vs AI+实拍混合、国内投流 vs 海外订阅、视频工具派之争、「AI 短剧是真需求还是伪风口」。不含: 传统实拍短剧制作、通用影视编剧(已有 scriptwriting skill)、短视频信息流投放(已有 short-video-ads skill)、纯 AI 视频底层技术研发。: top builders' mental models, tool stack, current workflows, jargon, and where to keep up. Trigger this skill when the user works on AI 短剧 (AI 微短剧) (从业者视角) — 用 AIGC 工具（AI 视频生成 / AI 脚本 / AI 生图 / AI 配音 / 对口型 / 角色一致性）制作竖屏微短剧并变现的新兴行业。覆盖: (a) 创作工作流 — 选题→剧本/分镜→AI 生图→图生视频(首尾帧/运镜/参考)→配音/对口型→剪辑/调色→成片，其中角色/场景一致性是第一性难题; (b) 工具栈 — 视频生成(可灵 Kling / 即梦 Seedance / 海螺 Hailuo / Vidu / Runway Gen / OpenAI Sora / Pika / Luma / Pixverse)、脚本(LLM)、生图(Midjourney/SD/即梦)、配音(TTS)、对口型、剪辑(剪映/CapCut); (c) 商业/变现 — 国内付费投流(IAP + ROI + 平台分账, 抖音/快手/红果/微信小程序短剧)与海外订阅(ReelShort/DramaBox/ShortMax/GoodShort)两套打法、品牌定制、成本结构; (d) 合规 — 中国《人工智能生成合成内容标识办法》(2025-09 强制 AI 标识)、广电微短剧备案与分类分层审核、版权与肖像权。主战场 = 抖音/快手/视频号/B站 + 海外短剧 App。学派分歧: 纯 AI vs AI+实拍混合、国内投流 vs 海外订阅、视频工具派之争、「AI 短剧是真需求还是伪风口」。不含: 传统实拍短剧制作、通用影视编剧(已有 scriptwriting skill)、短视频信息流投放(已有 short-video-ads skill)、纯 AI 视频底层技术研发。 problems and wants industry-grade thinking, tool selection, or workflow guidance. 触发词：「ai 短剧」「ai 微短剧」「ai short drama」「ai 短剧制作」「ai 短剧工作流」
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Field observation, data collection, and research methods for geographic inquiry. Covers site selection and sampling strategies, field observation techniques (landscape reading, transects, quadrats), survey and interview methods for human geography, GPS and field mapping, environmental monitoring and instrumentation, data recording and field notebooks, ethical considerations in fieldwork, and the integration of field data with GIS analysis. Use when planning geographic field research, designing data collection protocols, evaluating field evidence, or connecting field observations to broader geographic analysis.
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Complement to alice-emacs-mods. Covers what alice does not — ghostel mastery, multi-daemon orchestration, cross-session coordination, debug/recovery harness, REPL-as-dynamical-citizen, QRTP distribution, strobe internals, and the hard-won lessons from spawning and debugging live REPLs under the server daemon. Read alongside alice-emacs-mods; together they tile the total Emacs-mod space on this machine.
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Audits a methods section against a 45-item reporting checklist synthesized from the APSA Experimental Section rubric, JARS-Quant, CONSORT, and DA-RT, covering pre-registration, recruitment, randomization and treatments, sample flow and attrition, sample-size justification, three-tier results labeling, conjoint reporting, validity, and open-science infrastructure. Use when checking whether a methods section reports enough, preparing a submission or replication archive, asking what CONSORT, JARS, or DA-RT require, or documenting a deviation from a pre-analysis plan. Writing that plan before data collection goes to pre-registration-writing.
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Prove geometric theorems using Euclidean axiomatic methods, coordinate geometry, or vector methods with rigorous step-by-step logical structure. Covers direct proof, proof by contradiction, coordinate proofs, vector proofs, and handling of special cases and degenerate configurations. Use when given a geometric statement to prove, verifying a conjecture, establishing a lemma, converting geometric intuition into a rigorous proof, or comparing the effectiveness of different proof methods.
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Consumer Goods Cloud setup: visit execution, retail execution, route planning, in-store task management, compliance checks, off-shelf detection, image recognition. NOT for territory planning and route optimization for sales reps - use integration/salesforce-maps-setup. NOT for B2B Commerce storefronts - use admin/b2b-commerce-store-setup.
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Track exact provenance for every operation on ENCODE data — tool versions, reference files, scripts, parameters, and timestamps — to enable publication-ready methods writing. Use when the user processes ENCODE files, runs any bioinformatics tool, creates filtered/merged datasets, runs pipelines, performs liftover, uses R/Python/Bash for analysis, or needs to document their analysis chain for reproducibility and publication. Also use when the user says "write me methods" to auto-generate methods sections from the provenance log. This skill implements comprehensive provenance documentation: every tool, every version, every reference file, every parameter, every accession — no shortcuts. Use this skill for ANY processing step, ANY file transformation, ANY analysis operation on ENCODE data.
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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.
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Expert-level formal methods covering formal specification, model checking, theorem proving, type theory, program verification, and formal languages.
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Analyze WAF (ModSecurity/AWS WAF/Cloudflare) logs to detect SQL injection attack campaigns. Parses ModSecurity audit logs and JSON WAF event logs to identify SQLi patterns (UNION SELECT, OR 1=1, SLEEP(), BENCHMARK()), tracks attack sources, correlates multi-stage injection attempts, and generates incident reports with OWASP classification.
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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.
The English summary is being prepared. Showing the original description.
Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.
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Plan literature searches, screen academic and technical sources, and combine findings into a cited review. Records search methods and exclusions, compares conflicting evidence, identifies research gaps, and checks references so readers can trace the review's claims.
Support import and export compliance by classifying goods under tariff codes, reviewing customs documents, and assessing restricted-party matches. Covers trade agreement eligibility, duty-saving options, and customs inquiries across the US, EU, UK, and Asia-Pacific.
Get guidance for fine-tuning large language models with Axolotl, adapting them through additional training. Use YAML configuration examples, dataset references, and training methods such as LoRA to set up training and investigate problems.
Analyze and modify refusal behavior in open-weight language models without retraining. Use OBLITERATUS to select methods suited to available hardware, compare approaches, and evaluate changes in refusal rates and response quality.
Create engineering retrospectives from Git history, covering delivered changes, work patterns, test code ratios, and frequently changed files. Review individual contributions and improvement opportunities, save metrics, and compare results with earlier periods.