Agent Skills Directory

Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items, collections, tags, and attachments via the Zotero Web API v3 or local API. Applies when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.

Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics, predicted post-trimming overlap, sample IDs, runtime versions and read retention, and guides selection of compatible taxonomic classifiers.

Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, and Qiskit ecosystem packages.

Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where physical assumptions, dimensions, and numerical convergence must be explicit.

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR optics/acquisition checks, particle-stack consistency, gold-standard half sets, soft-mask validation, diagnostic Fourier shell correlation, and restart guidance.

Supports multivariate severity assessment and exploratory endpoint-time score forecasting for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting. Use when combining welfare readouts — body weight or weight loss, body temperature, clinical or nesting scores, biomarkers, activity, heart rate, burrowing, wheel running — into one severity score per animal per day, when asking which animals are at risk of reaching a humane endpoint at a specified future observation time, when defining attention/danger zones or thresholds on a severity scale by kernel density estimation, or when reporting severity for a 3Rs, refinement, animal-welfare, or EU Directive 2010/63/EU severity-assessment context. Covers directionality ("turned" variables), baseline normalization, reference sets, RELSA weights, ARIMA prediction intervals, and RMSE/PICP/MPIW evaluation.

Supports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including opportunity-specific requirements, aims, review criteria, budgets, broader impacts, forms, and resubmissions. Use for investigator-authored grant development, compliance matrices, and proposal critiques.

Compiles current scholarly evidence for a scientific manuscript or research brief when the user explicitly asks to gather literature, references, background evidence, competing findings, or a manuscript research packet. Uses Parallel Search by default, Parallel Extract for source retrieval, Parallel Research for explicitly deep/exhaustive work, optional explicit Parallel Chat, and optional Perplexity only when requested or allowed as a failure fallback.

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure.

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.

Provides qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls. Never use for ranking people or consequential decisions.

Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs. Use for early-stage research brainstorming or prioritizing candidate directions; hand off empirical validation, study design, ethics or regulatory review, and clinical questions to appropriate experts or skills.

Evaluates scientific claims and evidence quality. Applies to experimental design validity, biases and confounders, statistical interpretation, evidence grading frameworks (GRADE, Cochrane Risk of Bias), and teaching critical analysis. Supports evidence appraisal and identifying flaws; formal peer review writing belongs to peer-review.

Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.7 Flash for quality review. Refines when the review requests improvement, with at most two generations. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

Builds slide decks and presentations for research talks. Used for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.

Creates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use it for figure design, multi-panel layouts, uncertainty and missing-data displays, color/contrast review, image metadata validation, and journal export planning.

Drafts, revises, and audits scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks. Use for manuscript sections, references, declarations, tables, figures, or submission preparation when scientific accuracy and traceability matter.

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Supports machine learning in Python with scikit-learn. Applies when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.

Use when deciding whether a Cherry Studio change needs an Agent Note, authoring or reviewing a Spec, recording a durable bug-fix decision, moving a note between proposed/implemented/rejected, or checking supersession and stacked Spec approval.

从当前安装包查询 Cherry Studio 产品信息并排查运行问题。当用户询问功能、路由、快捷键、Provider、语言、Agent、频道、定时任务、Code CLI、当前版本，或报告运行错误、连接失败、配置异常并需要诊断时触发。

Control the user's visible Agent browser: navigate, click, type, screenshot, debug. Needs the Browser setting.

Drive native apps via Computer Use: open, inspect, type, click, screenshot. Needs OS permissions; respect user stop.

Develop, fix, profile, and test PRs in a tracked Cherry Studio Electron instance. Use for implementation, UI and interaction work, runtime debugging, DevTools inspection, performance analysis, and interactive PR verification with a test report. Reuse a verified workspace instance and manage its lifetime according to the selected workflow.

Run Cherry Studio critical-path system regression tasks through the repository-owned Playwright E2E workflow. Use for full regression, release acceptance, development-branch system validation, or a named cherry-regression-test task on GitHub-hosted macOS and Windows runners.

用户要求搜索、安装、查看或卸载 Skill，或内置能力不足时使用：先 search_skills，再 install_skill；无结果用 skill-creator 创建。

Use when Cherry Studio 用户希望报告、提交或整理 BUG、UI/UX 问题或功能建议，但未明确要求创建 GitHub Issue。

Cherry tool routing: bun, uv, rg, knowledge, memory, schedules, skills, MCP, web. Read before shell workarounds.

Recommend Claude Code automations (hooks, subagents, skills, plugins, MCP) and review an existing setup.

Run Antigravity CLI non-interactively for coding tasks. Use when the user asks to delegate work to Antigravity.

Run Claude Code non-interactively for coding tasks. Use when the user asks to delegate work to Claude Code.

Run Codex CLI non-interactively for coding tasks. Use when the user asks to delegate work to Codex.

Run DeepSeek Harness non-interactively for coding tasks. Use when the user asks to delegate work to it.

Run Gemini CLI non-interactively for coding tasks. Use when the user asks to delegate work to Gemini.

Run GitHub Copilot CLI non-interactively for coding tasks. Use when the user asks to delegate work to Copilot.

Run Hermes Agent non-interactively for local coding tasks. Use when the user asks to delegate work to Hermes.

Run Kimi Code non-interactively for coding tasks. Use when the user asks to delegate work to Kimi Code.

Run MiniMax Code non-interactively for coding tasks. Use when the user asks to delegate work to MiniMax Code.

Run the local OpenClaw agent non-interactively. Use when the user asks to delegate a bounded task to OpenClaw.

Run OpenCode non-interactively for coding tasks. Use when the user asks to delegate work to OpenCode.

Run Pi non-interactively for repository tasks. Use when the user asks to delegate analysis or implementation to Pi.

Run the Qoder CLI non-interactively with structured output. Use when the user asks to delegate a coding task to Qoder.

Run Qwen Code non-interactively for coding tasks. Use when the user asks to delegate work to Qwen Code.

Create a new skill in the current repository. Use when the user wants to create/add a new skill, or mentions creating a skill from scratch. This skill follows the workflow defined in .agents/skills/README.md and helps scaffold, validate, and sync new skills.

Use when writing, restructuring, auditing, or reviewing Cherry Studio repository documentation, READMEs, JSDoc, comments, Agent instructions, or paired English/Chinese docs, including source-linked documentation impact checks.

将成功解决的用户问题收录到 FAQ 知识库。问题解决后自动判断是否收录。也可以在用户说"收录到 FAQ"、"记录这个问题"、"add to FAQ"时手动触发。

Use when asked to find or plan Cherry Studio cleanup, simplification, refactoring, dead-code removal, duplicated state removal, unnecessary APIs, speculative generality, or library replacements, especially when the result should become evidence-backed proposed Agent Notes.