YuukiAS
- 200 skills
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- 6 hours ago last updated
- ▌ Clinical Reports · yuukias bundleDraft clinical case reports, diagnostic summaries, trial reports, SOAP/H&P/discharge-style documentation, and de-identified medical report templates with privacy, source, and guideline checks.
- ▌ Scientific Figure QA · yuukias bundleAudit scientific figures for publication readiness, accessibility, grayscale readability, export quality, and venue visual constraints.
- ▌ Academic Paper Writer Pro · yuukias bundle学术论文排版、OCR恢复、DOCX/Markdown整理和模板化交付工作流。用于扫描 PDF、DOC/DOCX、Markdown 到 Word/PDF 的结构修复、断点恢复、参考文献整理和最终文件验收；内容写作、审稿和事实保真应路由到 research-writing 与 writing-fidelity。
- ▌ Openai Docs · yuukias bundleUse for openai docs workflows when the task directly names this tool or domain. Prefer narrower project skills or umbrella retrieval skills when the task is only a lookup.
- ▌ Esm · yuukias bundleComprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations).
- ▌ Gtars · yuukias bundleHigh-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
- ▌ Opentargets Database · yuukiasArchived provider note for OpenTargets lookup. Use bioinformatics-database-retrieval for active project routing.
- ▌ Scientific Schematics · yuukias bundleCreate publication-quality scientific diagrams and schematics using configured image-generation and review providers. Use when papers, grants, presentations, posters, or educational materials need source-faithful visual illustrations, prompt planning, quality review, and iterative refinement.
- ▌ Nature Manuscript Workflow · yuukias bundlePlan, draft, revise, and audit broad-journal or high-impact manuscripts, including claim framing, figure logic, data availability, submission readiness, and reviewer response. Use for story-driven journal strategy, broad-audience manuscript framing, figure-to-claim alignment, and Nature-family targets when explicit.
- ▌ Business Presentations · yuukias bundlePlan business, executive, product, operations, market, client, strategy, pitch, and decision decks. Use when the audience is non-technical or the deck asks for a decision, resource, proposal, or business update.
- ▌ Research Presentations · yuukias bundlePlan evidence-first research and technical presentations from papers, repo evidence, Markdown reports, Asteria or TRACE exports, code results, figures, and existing decks. Use for group meetings, supervisor discussions, seminars, conferences, journal clubs, defenses, and scientific project updates.
- ▌ Research Paper Workflow · yuukias bundleFormal manuscript planning, drafting, revision, reviewer-style critique, rubric scoring, rebuttal, supplement, venue, and LaTeX coordination; route literature discovery and citation checks to literature-and-citations.
- ▌ Frontend Visual Systems 2 · yuukias bundleFrontend visual direction, design tokens, typography, palette, icon, layout, density, and motion brief.
- ▌ Tiledbvcf · yuukias bundleEfficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
- ▌ Flowio · yuukias bundleParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
- ▌ Geniml · yuukias bundleThis skill should be used when working with genomic interval data (BED files) for machine learning tasks. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
- ▌ Exploratory Data Analysis · yuukias bundlePerform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics.
- ▌ Implementation React Tailwind · yuukias bundleImplement production-ready frontend code with React, TypeScript, Tailwind CSS, and shadcn/ui. Use for components, pages, dashboards, forms, tables, navigation, themes, and responsive UI implementation.
- ▌ Markdown Mermaid Writing · yuukias bundleMarkdown and Mermaid diagram writing for reports, architecture notes, methods, workflows, and scientific documentation when structure or relationships need a diagram. Use for flowcharts, pipelines, dependency maps, timelines, and evidence maps; ordinary prose reports do not require diagrams.
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- ▌ Skill Creator · yuukias bundleGuide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations.
- ▌ Scvi Tools · yuukias bundleDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
- ▌ Scientific Critical Thinking · yuukias bundleEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
- ▌ Get Available Resources · yuukias bundleThis skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space).
- ▌ Render Chinese Math PDF · yuukias bundleRender and validate Chinese or mixed Chinese/English mathematical Markdown/LaTeX as PDF. Use for CJK text, Unicode math, equations, tables, Pandoc/XeLaTeX, TeX font/cache failures, citation cleanup, or readable PDF QA.
- ▌ Literature And Citations · yuukias bundleCurrent paper lookup, literature synthesis, single-paper evidence cards, citation support checks, BibTeX and reference metadata hygiene, and Zotero-oriented workflows.
- ▌ Statistical Visualization · yuukias bundleStatistical result visualization with Matplotlib and Plotly. For publication-ready figure palettes, venue figure QA, and manuscript figure styling, use the scientific-visualization plugin.
- ▌ Research Product Frontend 2 · yuukias bundleHigh-density research product frontend planning for imaging, phenotype, model comparison, provenance, and experiment interfaces.
- ▌ Plugin Creator · yuukias bundleCreate and scaffold plugin directories for Codex with a required `.codex-plugin/plugin.json`, optional plugin folders/files, and baseline placeholders you can edit before publishing or testing.
- ▌ Zarr Python · yuukias bundleChunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
- ▌ Arboreto · yuukias bundleInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
- ▌ Pydeseq2 · yuukias bundleDifferential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
- ▌ Scientific Visualization · yuukias bundleMeta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell).
- ▌ Responsive Accessibility Review · yuukias bundleReview and fix frontend responsiveness, accessibility, usability, keyboard behavior, text fitting, contrast, and visual regressions. Use before shipping UI or when asked to improve UX quality.
- ▌ Data Analysis Python · yuukias bundlePython data analysis workflows with EDA, Polars, scikit-learn, and symbolic math.
- ▌ Scientific Slides · yuukiasBuild slide decks and presentations for research talks. Use this 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.
- ▌ Skill Installer · yuukias bundleInstall external Codex skills from curated lists or GitHub repo paths. Use for third-party skill downloads; for AI_Skills_Collection installs prefer ai-skills repo/user targets and treat codex-home as explicit legacy compatibility.
- ▌ Deeptools · yuukias bundleNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
- ▌ Bayesian Modeling · yuukias bundleBayesian and statistical modeling workflows with PyMC, diagnostics, simulation, and model reporting.
- ▌ Polars Bio · yuukias bundleHigh-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.
- ▌ Biopython · yuukias bundleComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
- ▌ Clinicaltrials Database · yuukiasArchived provider note for ClinicalTrials.gov lookup. Use research or clinical workflow skills for active project routing.
- ▌ Publication Figure Palettes · yuukias bundleChoose publication figure palettes, contextual Notion-derived style candidates, presets, and snippets with provenance and experimental gates.
- ▌ Etetoolkit · yuukias bundlePhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
- ▌ Scikit Bio · yuukias bundleBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
- ▌ Clinical Decision Support · yuukias bundleProduce group-level clinical decision support, cohort evidence summaries, biomarker-stratified analyses, and guideline-style recommendation documents. Use for research, pharmaceutical, or policy documents, not bedside individual care.
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- ▌ Phylogenetics · yuukias bundleBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
- ▌ Dnanexus Integration · yuukias bundleDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
- ▌ Latchbio Integration · yuukias bundleLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
- ▌ Medical Imaging Deep Learning · yuukias bundleUse for medical-imaging deep learning tasks involving segmentation, MONAI/nnU-Net baselines, registration or warping, temporal/video imaging, missing-modality fusion, proposal/cascade/refinement models, external method adaptation, and validation evidence gates.
- ▌ Clinical Guideline Checking · yuukias bundleCheck clinical guideline claims against current authoritative sources, jurisdictions, population boundaries, recommendation strength, and update dates before using them in medical documents.
- ▌ Publication Figures · yuukias bundlePublication figure orchestration with contextual palette discovery, Matplotlib, Seaborn, Plotly, and export-ready layout.
- ▌ Neuropixels Analysis · yuukias bundleNeuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology.
- ▌ Medical Imaging Classical Features · yuukias bundleUse when enforcing reproducible medical-imaging preprocessing, physical-space geometry, classical registration baselines, radiomics protocols, or DICOM SEG/SR provenance.
- ▌ Medical Literature Evidence Review · yuukias bundleReview medical literature evidence with dated source notes, evidence hierarchy, population applicability, uncertainty, and safety boundaries. Use for medical evidence summaries, not direct care advice.
- ▌ Find · yuukiasQuickly find pages or databases in Notion by title keywords. Returns precise matches rather than comprehensive results.
- ▌ Medical Imaging Terminology Measurement · yuukias bundleUse medical imaging terminology and measurement conventions with source checks, modality-specific caveats, structured reporting boundaries, and uncertainty language.
- ▌ Search · yuukiasSearch the user's Notion workspace using the Notion MCP server. Use for finding pages, databases, and content by keywords or natural-language queries.
- ▌ Bioinformatics Database Retrieval · yuukias bundleUse for gene, protein, pathway, variant, expression, disease, and structure database lookups. Prefer workflow-specific skills for scanpy, scvi-tools, pysam, or DICOM work.
- ▌ Tasks Plan · yuukiasCreate an implementation plan from a Notion task or specification. Breaks down requirements into actionable steps with estimates and dependencies.
- ▌ Create Page · yuukiasCreate a new Notion page, optionally under a specific parent. Automatically structures content based on page type (meeting notes, project pages, etc.).
- ▌ Create Task · yuukiasCreate a new task in the user's Notion tasks database with sensible defaults for due date, status, owner, and project.
- ▌ Tasks Build · yuukiasBuild a task from a Notion page URL. Fetches task details, marks it in progress, implements the work, and updates status in Notion.
- ▌ Tasks Setup · yuukiasSet up a Notion task board for tracking tasks. Guides users through using a template or connecting an existing board.
- ▌ Database Query · yuukiasQuery a Notion database by name or ID and return structured, readable results with optional filters and sorting.
- ▌ Knowledge Capture · yuukiasTransform conversations and discussions into structured documentation pages in Notion. Captures insights, decisions, and knowledge from chat context with proper organization and linking.
- ▌ Tasks Explain Diff · yuukiasGenerate a rich Notion document explaining code changes. Creates comprehensive documentation with background, intuition, code walkthrough, and verification steps.
- ▌ Create Database Row · yuukiasInsert a new row into a specified Notion database using natural-language property values. Handles property name matching and validation.
- ▌ Meeting Intelligence · yuukiasPrepare meeting materials by gathering context from Notion, enriching with research, and creating both an internal pre-read and external agenda saved to Notion.
- ▌ Research Documentation · yuukiasSearch across your Notion workspace, synthesize findings from multiple pages, and create comprehensive research documentation with proper citations and actionable insights.
- ▌ Spec To Implementation · yuukiasTurn product or tech specs into concrete Notion tasks. Breaks down spec pages into detailed implementation plans with clear tasks, acceptance criteria, and progress tracking.
- ▌ Modal · yuukias bundleRun Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.
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- ▌ Pufferlib · yuukias bundleHigh-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack).
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- ▌ Aeon · yuukias bundleThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search.
- ▌ Dask · yuukias bundleDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
- ▌ Shap · yuukias bundleModel interpretability and explainability using SHAP (SHapley Additive exPlanations). Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
- ▌ Vaex · yuukias bundleUse this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM.
- ▌ Ocr Kb · yuukias bundle长文档 OCR、扫描 PDF 恢复、公式/表格/图注提取、断点续跑和 DOCX/Markdown 交付工作流。用于把 PDF 页面安全转成可编辑文本并做质量核查；内部处理模式可记录为 OCR，但用户不需要说旧 pipeline 名。
- ▌ Transformers · yuukias bundleThis skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks.
- ▌ Pymoo · yuukias bundleMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
- ▌ Sympy · yuukias bundleUse this skill when working with symbolic mathematics in Python. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
- ▌ Matlab · yuukias bundleMATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code.
- ▌ Polars · yuukias bundleFast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.
- ▌ PDF · yuukias bundleUse this skill whenever the user wants to do anything with PDF files. If the user mentions a .pdf file or asks to produce one, use this skill.
- ▌ Slurm Workflows · yuukias bundlePlan, submit, monitor, diagnose, and safely iterate Slurm jobs with generic resource estimation, job arrays, log/scratch layout, queue inspection, failure classification, and optional race execution policy supplied by a site profile.
- ▌ Pyzotero · yuukias bundleInteract with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3.
- ▌ Hypogenic · yuukias bundleAutomated 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).
- ▌ DOCX · yuukias bundleUse this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill.
- ▌ XLSX · yuukias bundleUse this skill any time a spreadsheet file is the primary input or output. Trigger especially when the user references a spreadsheet file by name or path — even casually (like \"the xlsx in my downloads\") — and wants something done to it or produced from it.
- ▌ Plotly · yuukias bundleInteractive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.
- ▌ Chinese Prose · yuukias bundle中文报告、README、Markdown/PDF 成稿、技术文档、科研说明、组会材料和“说人话”终审。任何中文 Markdown/PDF/报告/README/面向用户或读者的中文内容都应自动触发本 skill，用于普通中文润色、中文为主、降低 AI 味/翻译腔/模板腔/宣传腔，并保护事实、数字、术语、命令、引用、实验结果和证据边界。
- ▌ Gget · yuukiasArchived quick bioinformatics lookup note. Use bioinformatics-database-retrieval for active database routing.
- ▌ Torch Geometric · yuukias bundleGraph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
- ▌ Networkx · yuukias bundleComprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
- ▌ Seaborn · yuukias bundleStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualization.
- ▌ PPTX · yuukias bundleUse this skill any time a .pptx file is involved in any way — as input, output, or both. Trigger whenever the user mentions \"deck,\" \"slides,\" \"presentation,\" or references a .pptx filename, regardless of what they plan to do with the content afterward.
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