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1. ▌
   Statistical Analysis Usage Guide · tools-only bundle

   Statistical analysis identifies metabolites associated with biological conditions. Methods range from simple univariate tests to multivariate models for biomarker discovery.
   7 repo stars
2. ▌
   Model Interpretation Usage Guide · tools-only bundle

   Explain machine learning predictions on omics data using SHAP values for global and local feature attribution, and LIME for model-agnostic explanations.
   7 repo stars
3. ▌
   R Markdown Reports Usage Guide · tools-only bundle

   R Markdown combines code, results, and narrative into reproducible documents. Output to HTML, PDF, Word, or presentations.
   7 repo stars
4. ▌
   Cell Cell Communication Usage Guide · tools-only bundle

   Cell-cell communication analysis identifies ligand-receptor interactions between cell types from scRNA-seq data to understand tissue organization, signaling networks, and intercellular coordination.
   7 repo stars
5. ▌
   Multi Omics Integration Pipeline Usage Guide · tools-only bundle

   This workflow integrates multiple molecular data types (transcriptomics, proteomics, metabolomics, etc.) to discover shared biological signals and cross-modal biomarkers.
   7 repo stars
6. ▌
   Imputation Qc Usage Guide · tools-only bundle

   Quality control of imputed data is essential before downstream analysis, as poor quality imputation can introduce false positives in GWAS and bias effect estimates.
   7 repo stars
7. ▌
   Molecular I O Usage Guide · tools-only bundle

   Read, write, and convert molecular file formats including SMILES, SDF, MOL2, and PDB. Includes structure standardization pipeline for consistent molecular representations.
   7 repo stars
8. ▌
   Spatial Cell Cell Communication Usage Guide · tools-only bundle

   This skill covers analyzing cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Identify which cell types are communicating and through which signaling pathways.
   7 repo stars
9. ▌
   Chip Seq Visualization Usage Guide · tools-only bundle

   Create heatmaps, profile plots, and genome browser-style visualizations for ChIP-seq data using deepTools (CLI), ChIPseeker (R), and Gviz (R).
   7 repo stars
10. ▌
    Transcription And Translation Usage Guide · tools-only bundle

    This skill enables AI agents to help you convert between DNA, RNA, and protein sequences using Biopython.
    7 repo stars
11. ▌
    Population Structure Usage Guide 2 · tools-only bundle

    Population structure analysis identifies genetic ancestry and stratification using PCA (continuous clustering) and ADMIXTURE (discrete ancestry proportions).
    7 repo stars
12. ▌
    Alphafold Predictions Usage Guide · tools-only bundle

    Download and analyze AI-predicted protein structures from the AlphaFold database, including confidence scores (pLDDT) and predicted aligned error (PAE) for assessing prediction quality.
    7 repo stars
13. ▌
    Feature Selection Usage Guide · tools-only bundle

    Select informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization.
    7 repo stars
14. ▌
    Blast Searches Usage Guide · tools-only bundle

    This skill enables AI agents to help you run BLAST searches against NCBI databases using Biopython, finding similar sequences to identify unknown genes or find homologs.
    7 repo stars
15. ▌
    Mixomics Analysis Usage Guide · tools-only bundle

    mixOmics provides multivariate methods for multi-omics integration, including both supervised (DIABLO, sPLS-DA) and unsupervised (sPLS, sPCA) approaches with sparse feature selection.
    7 repo stars
16. ▌
    Metabolomics Pipeline Usage Guide · tools-only bundle

    This workflow processes raw mass spectrometry data through peak detection, alignment, normalization, statistical analysis, and pathway interpretation.
    7 repo stars
17. ▌
    Spatial Preprocessing Usage Guide · tools-only bundle

    This skill covers quality control, filtering, normalization, and feature selection for spatial transcriptomics data using Squidpy and Scanpy.
    7 repo stars
18. ▌
    Count Matrix Ingestion Usage Guide · tools-only bundle

    Load gene expression count matrices from various quantification tools (featureCounts, Salmon, kallisto, STAR, HTSeq, 10X) into pandas DataFrames for downstream analysis.
    7 repo stars
19. ▌
    Tree Visualization Usage Guide · tools-only bundle

    This skill creates publication-quality phylogenetic tree figures using Bio.Phylo's matplotlib integration. It supports customizing labels, colors, and exporting to various image formats.
    7 repo stars
20. ▌
    Cnv Visualization Usage Guide · tools-only bundle

    Effective CNV visualization helps identify patterns, validate calls, and communicate findings. This guide covers genome-wide profiles, region-specific plots, and cohort-level comparisons.
    7 repo stars
21. ▌
    Pathogen Typing Usage Guide · tools-only bundle

    Identify bacterial strain types using MLST, cgMLST, and SNP-based approaches for outbreak investigation and surveillance.
    7 repo stars
22. ▌
    Fragment Analysis Usage Guide · tools-only bundle

    Analyze cfDNA fragment size distributions and fragmentomics patterns for cancer detection. Extract nucleosome positioning signals and DELFI-style fragmentation profiles.
    7 repo stars
23. ▌
    Methylation Based Detection Usage Guide · tools-only bundle

    Analyze cfDNA methylation patterns for cancer detection and tissue-of-origin analysis. Uses bisulfite sequencing or cfMeDIP-seq for methylation profiling.
    7 repo stars
24. ▌
    Reactome Pathway Enrichment Usage Guide · tools-only bundle

    ReactomePA provides pathway enrichment analysis using the Reactome database, a curated peer-reviewed knowledgebase of biological pathways with deep hierarchy and reaction-level detail.
    7 repo stars
25. ▌
    Cnvkit Analysis Usage Guide 2 · tools-only bundle

    CNVkit is the standard tool for detecting copy number variants from targeted sequencing (exome, gene panels). It uses both on-target and off-target reads to infer copy number across the genome.
    7 repo stars
26. ▌
    Gene Id Mapping Usage Guide · tools-only bundle

    Convert between different gene identifier systems (Ensembl, Symbol, Entrez, UniProt) using mygene, biomaRt, and org.db packages for cross-database integration.
    7 repo stars
27. ▌
    Complete MCP Setup Guide MCP 2025 · tools-only bundle

    Step-by-step guide to set up the Skill Seeker MCP server with 5 supported AI coding agents.
    7 repo stars
28. ▌
    Technology Evaluation Metrics · tools-only bundle

    Detailed metrics and calculations used in technology stack evaluation.
    7 repo stars
29. ▌
    MCP Server Configuration Guide · tools-only bundle

    How to configure Aleph as an MCP server in all major MCP-compatible clients: Cursor, VS Code, Claude Desktop, Codex CLI, Windsurf, Kimi CLI, and others.
    7 repo stars
30. ▌
    Complete MCP Setup Guide MCP 2025 2 · tools-only bundle

    Step-by-step guide to set up the Skill Seeker MCP server with 5 supported AI coding agents.
    7 repo stars
31. ▌
    MCP Server Configuration Guide 2 · tools-only bundle

    This guide explains how to properly configure aleph as an MCP server in all major MCP-compatible clients: Cursor, VS Code, Claude Desktop, OpenAI Codex, Windsurf, and others.
    7 repo stars
32. ▌
    AI Tool Protocol Scan · tools-only bundle

    A.I.G leverages AI agents for comprehensive MCP Server and Skills security assessment, supporting both source code audits and remote URL scanning.
    7 repo stars
33. ▌
    Database Archival System · tools-only bundle

    Implement production-ready data archival strategies for PostgreSQL and MySQL that move historical records to archive tables or cold storage (S3, Azure Blob, GCS) with automated retention policies, compression…
    7 repo stars
34. ▌
    Structure I O Usage Guide · tools-only bundle

    This skill handles reading, writing, and downloading protein structure files. It supports PDB, mmCIF, MMTF, and BinaryCIF formats, with tools for downloading structures from RCSB PDB and extracting metadata.
    7 repo stars
35. ▌
    Agentkits Marketing Usage Guide · tools-only bundle

    Complete guide to using agentkits-marketing for production marketing workflows.
    7 repo stars
36. ▌
    Project Structure Reference · tools-only bundle

    The Definitions object is the entry point for all Dagster objects.
    7 repo stars
37. ▌
    Go Project Structure · tools-only bundle

    Best for small applications, CLIs, microservices with fewer than ~10 handlers, and projects where a single developer or small team owns the entire codebase.
    7 repo stars
38. ▌
    Project Structure Reference 2 · tools-only bundle

    The Definitions object is the entry point for all Dagster objects.
    7 repo stars
39. ▌
    Structure Analysis Summary · tools-only bundle

    The Structure Agent has completed a comprehensive depth 0 analysis of the TunaCode source code directory at /src/.
    7 repo stars
40. ▌
    Mermaid Hover Tooltip Fix · tools-only bundle

    When testing the Mermaid workflow diagram at http://localhost:8000/microsims/sims/basic/#workflow-example-microsim-creation, the hover tooltips were not appearing.
    7 repo stars
41. ▌
    MCP Prefix Issue In Claude Code · tools-only bundle

    The skills-lister MCP server is correctly implemented and configured, but Claude Code is not exposing the MCP tools with the required mcp__ prefix.
    7 repo stars
42. ▌
    Mental Models Reference · tools-only bundle

    Conceptual models that sharpen reasoning across all modes. Apply before analysis to frame the problem correctly.
    7 repo stars
43. ▌
    No More Context Bloat With MCP Manager Subagent Plus MCP · tools-only bundle

    When I finished reading Anthropic’s “Code execution with MCP” article, a sudden idea flashed in my mind
    7 repo stars
44. ▌
    Gas Fee Optimizer · tools-only bundle

    You are a gas fee optimization specialist. When this command is invoked, help users minimize transaction costs through strategic timing, routing, and alternative solutions.
    7 repo stars
45. ▌
    Database Partition Manager · tools-only bundle

    Design, implement, and manage table partitioning strategies for massive datasets with automated partition maintenance, query optimization, and data lifecycle management.
    7 repo stars
46. ▌
    MCP Integration 3 · tools-only bundle

    Model Context Protocol (MCP) integration for connecting Claude Code to external tools and services.
    7 repo stars
47. ▌
    Migration Guide Connected App External Client App 2 · tools-only bundle

    Step-by-step guide for migrating from Connected Apps to External Client Apps (ECAs).
    7 repo stars
48. ▌
    The Cornerstone Lbyl Over Eafp · tools-only bundle

    This is the single most important rule in dignified Python. Every pattern below flows from this principle.
    7 repo stars
49. ▌
    Senhasegura MCP Tools Integration · tools-only bundle

    Guide for integrating senhasegura with Claude Code using MCP (Model Context Protocol) tools.
    7 repo stars
50. ▌
    MCP Integration 4 · tools-only bundle

    OpenAkita supports the Model Context Protocol (MCP) for connecting to external services.
    7 repo stars
51. ▌
    MCP Integration 5 · tools-only bundle

    Model Context Protocol (MCP) enables AI assistants like Claude to interact with external tools and data sources. This guide covers setting up the Airbyte Agent MCP server for use with Claude Code and Claude Desktop.
    7 repo stars
52. ▌
    MCP Integration 6 · tools-only bundle

    Model Context Protocol (MCP) enables AI assistants like Claude to interact with external tools and data sources. This guide covers setting up the Airbyte Agent MCP server for use with Claude Code and Claude Desktop.
    7 repo stars
53. ▌
    Migration Guide To Shadcn UI · tools-only bundle

    This guide helps you migrate from other UI libraries to shadcn/ui.
    7 repo stars
54. ▌
    Mermaid Quick Reference 2 · tools-only bundle

    Quick reference guide for Mermaid diagram syntax used in sf-diagram.
    7 repo stars
55. ▌
    Conversation Turn Flow · tools-only bundle

    This document maps how a conversation turn flows through the system from user input to agent response to UI display.
    7 repo stars
56. ▌
    Conversation Turn Flow 2 · tools-only bundle

    This document maps how a conversation turn flows through the system from user input to agent response to UI display.
    7 repo stars
57. ▌
    MCP Server Integration · tools-only bundle

    This guide explains how to benchmark your MCP (Model Context Protocol) server with mcpbr.
    7 repo stars
58. ▌
    MCP Server Integration 2 · tools-only bundle

    MCP (Model Context Protocol) servers allow you to extend Claude's capabilities with custom tools and functions.
    7 repo stars
59. ▌
    Migration Guide Environment Variable Updates · tools-only bundle

    Starting with version 2.2.0, all environment variables have been renamed from VOICEMODE prefix to VOICEMODE_ prefix to reflect the project's new name.
    7 repo stars
60. ▌
    Pyhealth Medical Code Translation · tools-only bundle

    Healthcare data uses multiple coding systems and standards. PyHealth's MedCode module enables translation and mapping between medical coding systems through ontology lookups and cross-system mappings.
    7 repo stars
61. ▌
    Skill Scaffold 52 · tools-only bundle

    This skill optimizes Exa costs: understanding pricing model (requests, content extraction), minimizing numResults to actual needs, selective content extraction (text vs highlights vs full), caching to reduce duplicate…
    7 repo stars
62. ▌
    Messaging API V2 Guide Miaw 2 · tools-only bundle

    This guide covers building custom clients for Messaging for In-App and Web (MIAW), enabling Agentforce and Service Cloud conversations outside of Salesforce.
    7 repo stars
63. ▌
    Agent Response Panel · tools-only bundle

    Agent text responses are rendered in styled panels matching the NeXTSTEP tool panel aesthetic. This provides visual consistency across all output types.
    7 repo stars
64. ▌
    SQL Query Builder 3 · tools-only bundle

    Generates optimized SQL queries from natural language descriptions, supporting SELECT, INSERT, UPDATE, DELETE with JOINs, indexes, and best practices.
    7 repo stars
65. ▌
    Pydantic Removal Contract · tools-only bundle

    This document defines the minimal internal contracts that must remain stable while replacing pydantic-ai: request loop responsibilities, canonical message shapes, tool lifecycle handling, persistence format, and…
    7 repo stars
66. ▌
    Meeting Structures For Developers · tools-only bundle

    Templates and structures for common software development meetings. Use these to run effective meetings and ensure productive outcomes.
    7 repo stars
67. ▌
    Microsim Add Icons 2 · tools-only bundle

    The microsim-add-icons skill adds clickable Creative Commons license and fullscreen navigation icons to the control region of an existing p5.js MicroSim.
    7 repo stars
68. ▌
    Class To Modern React Migration Guide · tools-only bundle

    Modern Next.js 13+ supports Server Components, which cannot use hooks.
    7 repo stars
69. ▌
    Skill Scaffold 56 · tools-only bundle

    This skill implements robust rate limit handling for FireCrawl API operations. It covers reading and respecting rate limit headers, implementing exponential backoff with jitter to avoid thundering herd problems, request…
    7 repo stars
70. ▌
    Microsim Standardization Skill 2 · tools-only bundle

    The microsim-standardization skill performs comprehensive audits and quality upgrades of MicroSim directories to ensure they meet documentation and structural standards.
    7 repo stars
71. ▌
    Skill Scaffold 55 · tools-only bundle

    This skill implements full website crawling with FireCrawl's crawl endpoint. It covers crawl configuration including max depth, URL include/exclude patterns, sitemap utilization, rate limiting, and page limits.
    7 repo stars
72. ▌
    Express To Nestjs Migration Guide · tools-only bundle

    Gradually replace Express routes with NestJS while both run simultaneously.
    7 repo stars
73. ▌
    Skill Scaffold 53 · tools-only bundle

    This skill optimizes Exa performance: implementing query result caching (Redis, in-memory), cache key strategies for search queries, optimal numResults configuration, content extraction option optimization, parallel…
    7 repo stars
74. ▌
    Research Pydantic AI To Alchemy Rs Migration · tools-only bundle

    Map out what needs to change to migrate from pydantic-ai to alchemy-rs for LLM API calls, while keeping Python for state management and agent loop.
    7 repo stars
75. ▌
    File Scaffold 119 · tools-only bundle

    This skill provides production-ready patterns for Clay enrichment operations. It covers singleton API client initialization, robust error handling with structured logging, batch processing for multiple records…
    7 repo stars
76. ▌
    Medical Journal Structured Abstract Examples · tools-only bundle

    Examples of structured abstracts for NEJM, Lancet, JAMA, and BMJ showing the labeled section format expected at medical journals.
    7 repo stars
77. ▌
    Skill Scaffold 54 · tools-only bundle

    This skill implements efficient batch processing for large URL lists with FireCrawl.
    7 repo stars
78. ▌
    Research Recent Major Changes Last 3 Days · tools-only bundle

    Document all major changes from the last 3 days of development (Jan 25-28, 2026), including merged PRs, architectural refactors, and new features.
    7 repo stars
79. ▌
    Coordinated Agents 7 · tools-only bundle

    You are the Research Orchestrator - coordinating swarm-style parallel information gathering.
    7 repo stars
80. ▌
    Pre Flight Checks · tools-only bundle

    startstream() clears _insertionanchor = None to prevent stale positioning. clear() also clears the anchor.
    7 repo stars
81. ▌
    Research Streaming Response And Panel Display In Tunacode · tools-only bundle

    Explain how streaming responses work in the TunaCode TUI and what panels are shown before the final answer. This includes understanding the dual-display architecture (streaming overlay vs.
    7 repo stars
82. ▌
    Research Insertbeforestream Tool Panel Investigation · tools-only bundle

    Investigate the insertbeforestream() implementation to understand why tool panels might not be appearing correctly during streaming, despite the reported fix.
    7 repo stars
83. ▌
    Research Tools Layer Cross Layer Import Analysis · tools-only bundle

    Full audit of tools layer imports from configuration, exceptions, constants, and types. Map which files, what logic, and why.
    7 repo stars
84. ▌
    Medical Terminology And Coding Standards 2 · tools-only bundle

    This reference provides comprehensive medical terminology, coding systems, abbreviations, and nomenclature standards. Use these guidelines to ensure accurate, standardized clinical documentation.
    7 repo stars
85. ▌
    Directory Structure 18 · tools-only bundle

    This skill provides advanced troubleshooting techniques for complex Ideogram issues. It covers deep API debugging, network analysis, response quality assessment, intermittent failure diagnosis, and edge case handling.
    7 repo stars
86. ▌
    Lsp Module · tools-only bundle

    Implements a minimal Language Server Protocol client to fetch diagnostic feedback (errors, warnings) from language servers.
    7 repo stars
87. ▌
    Lsp Configuration Reference · tools-only bundle

    Complete guide for configuring Language Server Protocol in this Neovim setup.
    7 repo stars
88. ▌
    Type Annotation · tools-only bundle

    In Swift, there are two kinds of types: named types and compound types. A named type is a type that can be given a particular name when it's defined. Named types include classes, structures, enumerations, and protocols.
    7 repo stars
89. ▌
    Algorand Python Types · tools-only bundle

    Algorand Python provides statically-typed representations of AVM (Algorand Virtual Machine) types. These types differ from standard Python types and are essential for writing correct smart contracts.
    7 repo stars
90. ▌
    LLM Configuration · tools-only bundle

    Configure LLM for semantic extraction (L0/L1 generation) and reranking.
    7 repo stars
91. ▌
    Supported Models · tools-only bundle

    IntentKit supports a wide range of LLM providers and models to give you flexibility in choosing the right model for your needs.
    7 repo stars
92. ▌
    LLM Inference · tools-only bundle

    LLM selects the best UI component to visualize that data, and also configures it by selecting which values from the data have to be shown.
    7 repo stars
93. ▌
    MCP Reference · tools-only bundle

    The Atlassian MCP does not currently support creating issue links. Use the bundled jira-link-issues script instead.
    7 repo stars
94. ▌
    Types Module · tools-only bundle

    Centralizes all type aliases, protocols, and dataclass definitions for type safety and consistency across the codebase.
    7 repo stars
95. ▌
    Constants Module · tools-only bundle

    Centralizes global constants, magic strings, UI text, error messages, and application-wide fixed values.
    7 repo stars
96. ▌
    LLM Integration Guide For Intentkit · tools-only bundle

    This guide provides comprehensive information for Large Language Models (LLMs) working with the IntentKit autonomous agent framework.
    7 repo stars
97. ▌
    MCP Overview · tools-only bundle

    import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; import Image from '@theme/IdealImage';
    7 repo stars
98. ▌
    MCP Overview 2 · tools-only bundle

    import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; import Image from '@theme/IdealImage';
    7 repo stars
99. ▌
    MCP Overview 3 · tools-only bundle

    import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; import Image from '@theme/IdealImage';
    7 repo stars
100. ▌
     MCP Model Context Protocol · tools-only bundle

     MCP is an open standard for connecting AI models to external services. Skill Compose uses MCP to extend agent capabilities beyond built-in tools — adding web search, Git operations, URL fetching, and more.
     7 repo stars