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Claude Skills by tools-only
github.com/tools-only19,166 skills18 installs6,168 views
- 572 Usage Guide 5241a1adBowtie2 is a fast and memory-efficient aligner for short reads. It supports both end-to-end and local alignment modes, making it versatile for ChIP-seq, ATAC-seq, and general short-read alignment.Votes: 0GitHub stars: 9
- 572 Usage Guide 573742efMAGeCK is the standard tool for analyzing pooled CRISPR screens. It handles count normalization, identifies significantly enriched/depleted genes, and performs pathway analysis.Votes: 0GitHub stars: 9
- 572 Usage Guide 671d0e5eMultiple methods exist for calling hits in CRISPR screens. The choice depends on screen design, reference data availability, and desired stringency.Votes: 0GitHub stars: 9
- 572 Usage Guide 68af5645This guide covers merging, concatenating, sorting, and comparing VCF files.Votes: 0GitHub stars: 9
- 572 Usage Guide 768a18a2Discover novel miRNAs and quantify known miRNAs using miRDeep2's de novo prediction algorithm based on secondary structure and read patterns.Votes: 0GitHub stars: 9
- 572 Usage Guide 78663edeSTAR (Spliced Transcripts Alignment to a Reference) is the most widely used RNA-seq aligner. It's extremely fast, supports splice-aware alignment, and can detect novel junctions with two-pass mode.Votes: 0GitHub stars: 9
- 572 Usage Guide 7e9b129dGenerate pileup data showing all reads covering each genomic position for variant calling and position-level analysis.Votes: 0GitHub stars: 9
- 572 Usage Guide 838580a4Taxonomic assignment classifies ASVs or OTUs to taxonomic ranks (Kingdom through Species) using reference databases like SILVA, GTDB, or UNITE.Votes: 0GitHub stars: 9
- 572 Usage Guide 902ba7e9Proximity operations help you find relationships between genomic features based on their distance. This skill covers finding nearest features (closest), searching within distance windows (window), and extending intervals (slop, flank).Votes: 0GitHub stars: 9
- 572 Usage Guide A299ffa1Process PacBio Iso-Seq data for full-length transcript discovery and isoform characterization.Votes: 0GitHub stars: 9
- 572 Usage Guide Fe4dd08bGenotype imputation predicts untyped variants using haplotype patterns from a reference panel, enabling increased variant density for GWAS, fine-mapping, and polygenic risk score calculation.Votes: 0GitHub stars: 9
- 584 Writer 1664b873You are a **deep research and scientific writing assistant** that combines AI-driven research with well-formatted written outputs. Create high-quality academic papers, literature reviews, grant proposals, clinical reports, and other scientific documents backed by comprehensive research and real, verifiable citations.Votes: 0GitHub stars: 9
- 584 Writer D3382e65You are a **deep research and scientific writing assistant** that combines AI-driven research with well-formatted written outputs. Create high-quality academic papers, literature reviews, grant proposals, clinical reports, and other scientific documents backed by comprehensive research and real, verifiable citations.Votes: 0GitHub stars: 9
- 585 Scientific Writer Init E755dd16Initialize the current project with Scientific Writer - a deep research and writing tool that combines AI-driven research with well-formatted written outputs.Votes: 0GitHub stars: 9
- 586 Development 345145eeThis document is for contributors and maintainers. It summarizes the package architecture, design decisions, and development workflow for Scientific Writer v2.7.0.Votes: 0GitHub stars: 9
- 587 Documentation Index 0962bfde**Scientific Writer v2.7.0** - Comprehensive documentation navigation guide. ---Votes: 0GitHub stars: 9
- 588 Scientific Skill Cae38a9f**Scientific Writer is a deep research and writing tool** that combines AI-driven deep research with well-formatted written outputs. The skills below power this capability—from conducting literature searches and verifying citations to generating publication-ready documents in various formats. This document provides an overview of all skills available in the Scientific Writer CLI.Votes: 0GitHub stars: 9
- 589 Implementation Summary 514cbe9bSuccessfully implemented a comprehensive clinical reports skill for the Claude Scientific Writer project.Votes: 0GitHub stars: 9
- 590 Skill Summary Adc7cf2bA comprehensive skill for using Microsoft's MarkItDown tool has been created for the Claude Scientific Writer. This skill enables conversion of 15+ file formats to Markdown, optimized for LLM processing and scientific workflows.Votes: 0GitHub stars: 9
- 592 Literature Search Strategies Ff637b4cComprehensive literature search is essential for grounding hypotheses in existing evidence. This reference provides strategies for both PubMed (biomedical literature) and general scientific search.Votes: 0GitHub stars: 9
- 593 Database Strategies 199c3b8eThis document provides comprehensive guidance for searching multiple literature databases systematically and effectively.Votes: 0GitHub stars: 9
- 594 Imrad Structure B70f52f1IMRAD (Introduction, Methods, Results, And Discussion) is the predominant organizational structure for scientific journal articles of original research. Adopted as the majority format since the 1970s, it is now the standard in medical, health, biological, chemical, engineering, and computer sciences.Votes: 0GitHub stars: 9
- 595 Features 28cba038This comprehensive guide covers all features available in Local Deep Research (LDR). > **Note**: This documentation is maintained by the community and may contain inaccuracies. While we strive to keep it up-to-date, please verify critical information and report any errors via [GitHub Issues](https://github.com/LearningCircuit/local-deep-research/issues).Votes: 0GitHub stars: 9
- 600 Reference A9ea8904This is the full reference documentation for the Airtable agent connector.Votes: 0GitHub stars: 9
- 600 Reference E5881e62This is the full reference documentation for the Airtable agent connector.Votes: 0GitHub stars: 9
- 600 Reference Ede69581This is the full reference documentation for the Airtable agent connector.Votes: 0GitHub stars: 9
- 629 Faq 06ff21f6> **Note**: This documentation is maintained by the community and may contain inaccuracies. While we strive to keep it up-to-date, please verify critical information and report any errors via [GitHub Issues](https://github.com/LearningCircuit/local-deep-research/issues).Votes: 0GitHub stars: 9
- 629 Faq 3a909ea1> **Note**: This documentation is maintained by the community and may contain inaccuracies. While we strive to keep it up-to-date, please verify critical information and report any errors via [GitHub Issues](https://github.com/LearningCircuit/local-deep-research/issues).Votes: 0GitHub stars: 9
- 630 Metrics Dashboard 77b850d2This guide covers the Metrics Dashboard for monitoring research performance, costs, and usage analytics.Votes: 0GitHub stars: 9
- 631 Search Engines 1bc1c03bLocal Deep Research integrates with multiple search engines to provide comprehensive research capabilities. This guide covers all available search engines, their specializations, and configuration details. > **Note**: This documentation is maintained by the community and may contain inaccuracies. While we strive to keep it up-to-date, please verify critical information and report any errors via [GitHub Issues](https://github.com/LearningCircuit/local-deep-research/issues).Votes: 0GitHub stars: 9
- 632 Database Schema A0f7fe68This document describes the database models and their relationships in Local Deep Research.Votes: 0GitHub stars: 9
- 632 Database Schema C2f9682eThis document describes the database models and their relationships in Local Deep Research.Votes: 0GitHub stars: 9
- 652 Top 10 Ai Agent Frameworks 2025 D04933f4*A comprehensive guide to the leading frameworks for building AI agents* --- The AI agent landscape has exploded with options for developers. Whether you're building RAG applications, multi-agent systems, or autonomous workflows, choosing the right framework can significantly impact your project's success. This guide objectively compares the top 10 AI agent frameworks based on architecture, use cases, and production readiness. ---Votes: 0GitHub stars: 9
- 659 Description Skill 56cc52bbThis skill should be used when users need to generate ideas, explore creative solutions, or systematically brainstorm approaches to problems. Use when users request help with ideation, content planning, product features, marketing campaigns, strategic planning, creative writing, or any task requiring structured idea generation. The skill provides 30+ research-validated prompt patterns across 14 categories with exact templates, success metrics, and domain-specific applications.Votes: 0GitHub stars: 9
- 659 Description Skill 5956003eAutonomous Refinement Loop for iterative skill improvement — Assess, Plan, Implement, Review, Repeat until converged. Machine-verifiable gates (R1-R10) replace human judgment at each phase. Use when refining skills through multiple autonomous iterations.Votes: 0GitHub stars: 9
- 659 Description Skill 6f321cc5Research and compare the Stateless Agent Methodology (SAM) against other methodologies using only verifiable reference material. Produce overlap/divergence analysis that is useful for comparing strategy, methodologies, and potential implementations, and for identifying weaknesses in the current SAM methodology while changes are still cheap. Creates structured comparison documents following the SAM comparison template, including terminology normalization + attribution notes.Votes: 0GitHub stars: 9
- 659 Description Skill 83caeeb0Autonomous Refinement Loop for iterative skill improvement — Assess, Plan, Implement, Review, Repeat until converged. Machine-verifiable gates (R1-R10) replace human judgment at each phase. Use when refining skills through multiple autonomous iterations.Votes: 0GitHub stars: 9
- 659 Description Skill 9d3ae7a4This skill should be used when users need to generate ideas, explore creative solutions, or systematically brainstorm approaches to problems. Use when users request help with ideation, content planning, product features, marketing campaigns, strategic planning, creative writing, or any task requiring structured idea generation. The skill provides 30+ research-validated prompt patterns across 14 categories with exact templates, success metrics, and domain-specific applications.Votes: 0GitHub stars: 9
- 659 Description Skill B89b4dfdKnowledge reference for Autonomous Refinement Loop research — pattern research into prerequisites for autonomous execution without synchronous human blocking gates. Defines failure categories, prerequisites, and conditions for replacing human judgment with machine-verifiable checks. Use when designing or evaluating autonomous agent loops, gate conditions, or HOOTL execution patterns.Votes: 0GitHub stars: 9
- 693 Stateless Software Engineering Framework 7e735de5**Date**: 2026-01-25 **Status**: Design Document **Purpose**: Define a constraint-driven development framework that compensates for LLM limitations through architectural structure rather than model capability ---Votes: 0GitHub stars: 9
- 693 Stateless Software Engineering Framework F6b12de7**Date**: 2026-01-25 **Status**: Design Document **Purpose**: Define a constraint-driven development framework that compensates for LLM limitations through architectural structure rather than model capability ---Votes: 0GitHub stars: 9
- 694 Hound 37570ca4**Research Date**: January 26, 2026 **Source URL**: <https://github.com/scabench-org/hound> **Academic Paper**: <https://arxiv.org/abs/2510.09633> **Version at Research**: Commit from October 15, 2025 (no tagged releases) **License**: Apache 2.0 ---Votes: 0GitHub stars: 9
- 695 Github Patterns 24444952**Research Date**: December 9, 2025 **Methodology**: Systematic search of GitHub repositories for Claude Code research agents, awesome lists, and multi-agent research workflows. ---Votes: 0GitHub stars: 9
- 695 Github Patterns Df38fb37**Research Date**: December 9, 2025 **Methodology**: Systematic search of GitHub repositories for Claude Code research agents, awesome lists, and multi-agent research workflows. ---Votes: 0GitHub stars: 9
- 696 Process And Comparison Methodology With References 7748bb92This document records the **actual process executed** to produce: - Output template file: `methodology_development/methodology_comparison_template.md` - Supporting research summary: delivered in-chat as “Stage 1: Research & Information Gathering” Goal: produce a reusable, universal comparison template grounded in **real-world comparison methodologies** (consumer, technical, business, academic), with an **AI-oriented pre-comparison reflection** and **bounded self-extension**. ---Votes: 0GitHub stars: 9
- 697 Sam Vs Octocode B8bacac9A comparative analysis of two approaches to improving LLM agent reliability through structured workflows. ---Votes: 0GitHub stars: 9
- 698 Feature Researcher 644ab486Researches feature requests and existing architecture documents to produce discovery context. Explores codebase patterns, identifies ambiguities, documents use scenarios, and surfaces questions for orchestrator resolution. Does NOT make technical implementation decisions.Votes: 0GitHub stars: 9
- 698 Feature Researcher Cadd1845Researches feature requests and existing architecture documents to produce discovery context. Explores codebase patterns, identifies ambiguities, documents use scenarios, and surfaces questions for orchestrator resolution. Does NOT make technical implementation decisions.Votes: 0GitHub stars: 9
- 699 Gaps Analysis 9fc3e939Analysis of the skill-research-process compared to repository best practices.Votes: 0GitHub stars: 9
- 699 Gaps Analysis Cf3eb885Analysis of the skill-research-process compared to repository best practices.Votes: 0GitHub stars: 9