denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
deepchem
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
chembl-database
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
scvi-tools
Deep 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.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
scanpy
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
geniml
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
biorxiv-database
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
financial_research
面向股票/行业/宏观的金融研究技能，结合结构化金融数据（OpenBB/AkShare）与多源信息验证，生成带引用与免责声明的研究报告。
deep_research
深度研究能力，支持多源搜索、信息聚合、引用回溯、文档上传分析。适用于市场调研、竞品分析、学术研究、技术选型、金融投研等场景。支持上传 PDF/Excel/Word 等文档，自动转换并提取关键信息。
feishu-doc-creator-with-permission
文档创建+权限管理子技能 - 在飞书创建文档并自动完成权限分配（添加协作者+转移所有权），两步原子操作。
feishu-logger
日志记录子技能 - 记录文档创建结果到日志文件，支持 Markdown 和 JSON 格式。
feishu-block-adder
块添加子技能 - 将解析后的块数据添加到飞书文档，分批处理，支持表格和普通块，**现在支持图片上传**。
feishu-md-parser
Markdown解析子技能 - 将Markdown文件解析为飞书文档块格式，输出JSON文件，支持25种块类型映射，**现在支持图片上传**。
feishu-doc-orchestrator
飞书文档创建主编排技能 - 将 Markdown 文件转换为飞书文档，编排多个子技能协作完成，支持25种飞书文档块类型。
feishu-doc-verifier
文档验证子技能 - 使用 Playwright 验证飞书文档是否创建成功。
vue-best-practices
Vue 3 and Nuxt performance optimization guidelines. This skill should be used when writing, reviewing, or refactoring Vue 3/Nuxt code to ensure optimal performance patterns. Triggers on tasks involving Vue components, Nuxt pages, data fetching, bundle optimization, or performance improvements.
pic-js
Guides writing Internet Computer canister integration tests with PicJS and PocketIC. Use when the user mentions PicJS, PocketIC, canister integration tests, or requests JavaScript/TypeScript tests for canisters.
icp-cli
Guides use of the Internet Computer (ICP) CLI (icp) v0.1.0 for local networks, builds, deploys, canister operations, identities, cycles/tokens, recipe system, environments, and advanced features. Use when the user asks about icp-cli, icp commands, canister deployment, local ICP network workflows, recipes, multi-environment deployments, or command help. Also use whenever dfx is mentioned so guidance always maps to icp.
forum-research
Research and read content on forum.dfinity.org (Discourse). Use when the user asks to browse, search, summarize, or analyze Dfinity forum topics or users. Read-only access with authenticated browsing and JSON endpoints.
clean-typescript
Write clean, efficient TypeScript code that follows common best practices
use-modern-browser-apis
Utilize built-in browser APIs (like Popover API, View Transitions etc) instead of building features manually via JavaScript
bun-first
Describes efficient usage of Bun and Bun APIs instead of Node.js (and its APIs)
modern-accessible-html-jsx
Write clean, modern, and highly accessible HTML & JSX code, using semantically correct elements and attributes
modern-best-practice-nextjs
Build modern Next.js apps with App Router and best practices
web-security
Enforce web security and avoid security vulnerabilities
modern-tailwind
Build clean, scalable UIs with Tailwind CSS using modern utilities and variants
modern-best-practice-react-components
Build clean, modern React components that apply common best practices and avoid common pitfalls like unnecessary state management or useEffect usage
agent-manager-skill
Manage multiple local CLI agents via tmux sessions (start/stop/monitor/assign) with cron-friendly scheduling.
baoyu-danger-gemini-web
Generates images and text via reverse-engineered Gemini Web API. Supports text generation, image generation from prompts, reference images for vision input, and multi-turn conversations. Use when other skills need image generation backend, or when user requests "generate image with Gemini", "Gemini text generation", or needs vision-capable AI generation.
baoyu-cover-image
Generates article cover images with 5 dimensions (type, palette, rendering, text, mood) combining 9 color palettes and 6 rendering styles. Supports cinematic (2.35:1), widescreen (16:9), and square (1:1) aspects. Use when user asks to "generate cover image", "create article cover", "make cover", or mentions "封面图".
baoyu-compress-image
Compresses images to WebP (default) or PNG with automatic tool selection. Use when user asks to "compress image", "optimize image", "convert to webp", or reduce image file size.
business-analyst
Master modern business analysis with AI-powered analytics,
busybox-on-windows
How to use a Win32 build of BusyBox to run many of the standard UNIX command line tools on Windows.
c-pro
Write efficient C code with proper memory management, pointer
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