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Claude Skills by tools-only
github.com/tools-only19,166 skills18 installs6,168 views
- 266 Usage Guide 68d25f44This workflow processes ATAC-seq data from raw FASTQ files to accessibility peaks, with optional differential analysis and transcription factor footprinting.Votes: 0GitHub stars: 9
- 266 Usage Guide 697cfa22This guide covers creating reproducible Jupyter notebooks with parameterization for automated analysis pipelines.Votes: 0GitHub stars: 9
- 266 Usage Guide 816944c8This workflow processes single-cell RNA-seq data from 10X Genomics Cell Ranger output to annotated cell types. It supports both Seurat (R) and Scanpy (Python) implementations.Votes: 0GitHub stars: 9
- 266 Usage Guide 87f7d496Structural variants (SVs) are genomic alterations typically >50bp that include deletions, insertions, inversions, duplications, and translocations. Short-read SV calling uses paired-end and split-read information to detect these events.Votes: 0GitHub stars: 9
- 266 Usage Guide 8b5fe2f9Complete gene regulatory network inference workflow from processed single-cell data to regulon discovery and perturbation simulation. Supports RNA-only analysis with pySCENIC (GRNBoost2 + RcisTarget + AUCell) and multiome analysis with SCENIC+ for enhancer-driven GRNs. Includes CellOracle for in silico perturbation simulation.Votes: 0GitHub stars: 9
- 266 Usage Guide 91d9b591Basecalling converts raw Nanopore signal data (FAST5/POD5) to nucleotide sequences. Dorado is the current production basecaller and should be used for all new analyses. Guppy is deprecated and no longer receiving updates.Votes: 0GitHub stars: 9
- 266 Usage Guide A8f9b8efGATK provides a robust, best-practices CNV calling workflow. It uses principal component analysis to denoise samples against a panel of normals and integrates allelic information for improved accuracy.Votes: 0GitHub stars: 9
- 266 Usage Guide B1d443c2Polishing improves assembly accuracy by using additional sequencing data to correct errors. Essential for long-read assemblies which have higher raw error rates.Votes: 0GitHub stars: 9
- 266 Usage Guide C438f645Complete time-course expression analysis workflow from expression matrix to temporal patterns and pathway enrichment. Covers temporal differential expression (limma splines or DESeq2 LRT), Mfuzz soft clustering of expression profiles, optional circadian rhythm detection with MetaCycle or CosinorPy, GAM trajectory fitting with mgcv, and per-cluster pathway enrichment with clusterProfiler. Supports both R and Python alternatives at each step.Votes: 0GitHub stars: 9
- 266 Usage Guide D5b8c5d0Complete environmental DNA metabarcoding workflow from raw amplicon sequences to biodiversity assessment and community ecology. Supports two processing paths: OBITools3 (CLI-based, optimized for eDNA) and DADA2 (R-based, ASV resolution). Includes contamination filtering with decontam, Hill number diversity analysis with iNEXT, and constrained ordination with vegan for community comparison. Handles all common eDNA markers (COI, 12S, ITS, rbcL, 18S).Votes: 0GitHub stars: 9
- 266 Usage Guide Fe19c1daThis workflow takes you from raw DNA sequencing FASTQ files to a filtered set of variant calls (SNPs and indels). It covers the entire process from quality control through alignment and variant calling.Votes: 0GitHub stars: 9
- 267 Automation 3dfb4b4cThe MCP Context Provider now includes comprehensive build automation to ensure code quality, consistent releases, and streamlined development workflows.Votes: 0GitHub stars: 9
- 267 Automation 4db36136| Pattern | When to Use | | ------------------------ | ------------------------------------------------- | | `AutomationCondition` | Modern asset-centric automation with conditions | | `ScheduleDefinition` | Fixed time intervals (daily, hourly, monthly) | | `@dg.schedule` decorator | Custom schedule logic with dynamic job selection | | `@dg.sensor` | Event-driven triggers (file changes, API updates) | | `PartitionsDVotes: 0GitHub stars: 9
- 268 Prototype 8a3b2a13You are helping a developer prototype a new Dagster implementation following best practices. The implementation requirements and working directory have been provided: $ARGUMENTSVotes: 0GitHub stars: 9
- 269 Plan 9cf192d7Start Manus-style file-based planning. Creates task_plan.md, findings.md, progress.md for complex tasks.Votes: 0GitHub stars: 9
- 271 Progress 75fde552<!-- ============================================================ [CUSTOMIZE] This is a template. Fill in your workflow details. ============================================================ --> > **Vision**: [CUSTOMIZE: One-sentence description of workflow goal] > **Last updated**: [Date] (Iteration 0) > **Status**: Not startedVotes: 0GitHub stars: 9
- 272 Security Scorecard A19e5df8This document explains our compliance status with OSSF Scorecard checks and documents any accepted risks or false positives.Votes: 0GitHub stars: 9
- 272 Security Scorecard Fed9e50eThis document explains our compliance status with OSSF Scorecard checks and documents any accepted risks or false positives.Votes: 0GitHub stars: 9
- 273 Ai Code Reviewer Setup 9e52b44bThis guide explains how to set up the automated AI PR review system using OpenRouter to analyze pull requests with your choice of AI model.Votes: 0GitHub stars: 9
- 274 Release Guide 99495a39Releases are now **fully automated** when PRs are merged to the `main` branch.Votes: 0GitHub stars: 9
- 275 Pr Requirements 03e587e4This repository enforces that all pull requests must be linked to an issue that has an assignee. PRs that don't meet this requirement are automatically closed.Votes: 0GitHub stars: 9
- 276 Human In The Loop Ai Agents 5225d5b3*Balancing automation with human oversight for safe, effective AI systems* --- Human-in-the-Loop (HITL) is a critical design pattern for AI agents. It ensures that humans remain in control of important decisions while still benefiting from AI automation. This guide covers everything you need to know about implementing HITL in agent systems. ---Votes: 0GitHub stars: 9
- 278 Readmeja 5aa40387> English version: [README.md](README.md) <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/b...Votes: 0GitHub stars: 9
- 278 Readmeja 76df3aa0> English: [README.md](README.md) <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/badge/lic...Votes: 0GitHub stars: 9
- 278 Readmeja 9e0ea8ec> English version: [README.md](README.md) <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/b...Votes: 0GitHub stars: 9
- 278 Readmeja A25c8ae6（fail-closed + HITL） <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/badge/license-Apache--...Votes: 0GitHub stars: 9
- 278 Readmeja Ac1dde06（fail-closed + HITL） <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/badge/license-Apache--...Votes: 0GitHub stars: 9
- 278 Readmeja C8bfa185> English version: [README.md](README.md) <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/b...Votes: 0GitHub stars: 9
- 278 Readmeja E5d1a15a> English version: [README.md](README.md) <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/b...Votes: 0GitHub stars: 9
- 278 Readmeja Fbbf06b3> English version: [README.md](README.md) <p align="center"> <a href="https://github.com/japan1988/multi-agent-mediation/stargazers"> <img src="https://img.shields.io/github/stars/japan1988/multi-agent-mediation?style=social" alt="GitHub Stars"> </a> <a href="https://github.com/japan1988/multi-agent-mediation/issues"> <img src="https://img.shields.io/github/issues/japan1988/multi-agent-mediation?style=flat-square" alt="Open Issues"> </a> <a href="./LICENSE"> <img src="https://img.shields.io/b...Votes: 0GitHub stars: 9
- 279 Workflow 7152f88cTo prepare the project for overnight development:Votes: 0GitHub stars: 9
- 279 Workflow A7a306ceComplete guide for the 4-phase conversion process.Votes: 0GitHub stars: 9
- 284 Sql Plugins Configuration Guide 530099b3This guide shows how to configure the SQL plugins through the web interface.Votes: 0GitHub stars: 9
- 285 Public Workspaces F6fe27bc**Version Implemented:** 0.229.001Votes: 0GitHub stars: 9
- 286 Pii Analysis Workflow 45d66f35**Fixed/Implemented in version: 0.229.072**Votes: 0GitHub stars: 9
- 287 Control Center Application Roles A4032d54Added two new application roles for finer-grained access control to the Control Center, enabling organizations to delegate administrative functions while maintaining security boundaries.Votes: 0GitHub stars: 9
- 288 Workflow Pdf Viewer Height Fix 0128d69a**Fixed in version:** 0.230.001Votes: 0GitHub stars: 9
- 289 Extraction Patterns 600795b3This reference provides detailed patterns for extracting expertise through strategic questioning and active listening. The goal is to transform implicit knowledge into explicit, documented expertise.Votes: 0GitHub stars: 9
- 290 Best Practices C8f32b35Guidelines for optimal skill usage and development.Votes: 0GitHub stars: 9
- 290 Best Practices F98e59311. [Overview](#overview) 2. [Core Principles](#core-principles) - [1. Reproducibility: Eliminate Manual Steps](#1-reproducibility-eliminate-manual-steps) - [2. Portability: Query Workbook Separation](#2-portability-query-workbook-separation) - [3. Find the True Source](#3-find-the-true-source) - [4. Future-Proofing: Design for Change](#4-future-proofing-design-for-change) - [5. Headers Before Everything](#5-headers-before-everything) - [6. Document and Organize](#6-document-andVotes: 0GitHub stars: 9
- 291 Methodology Cf22d359How to effectively combine TRIZ with Large Language Models for systematic innovation. ---Votes: 0GitHub stars: 9
- 293 Implementation Workflow 16d71200Complete workflow for building production-ready Dagster implementations following best practices.Votes: 0GitHub stars: 9
- 296 Discussion 2 Content 97252ffdI've implemented session management patterns from Anthropic's article ["Effective harnesses for long-running agents"](https://www.anthropic.com/engineering/effective-harnesses-for-long-running-agents) in the **`feature/anthropic-patterns`** branch.Votes: 0GitHub stars: 9
- 297 Migration 2b56cf16Version 2.0.0 adds hooks integration and enhanced templates while maintaining backward compatibility with existing workflows.Votes: 0GitHub stars: 9
- 298 Release 3485bb27Create GitHub release with automated notesVotes: 0GitHub stars: 9
- 298 Release A5957614本文档记录 OpenAkita 的标准发版操作流程。**所有贡献者（包括 AI 辅助工具）发版时必须遵循此流程。** ---Votes: 0GitHub stars: 9
- 298 Release D0ccd98bThis document explains how to create releases for mcpbr, both manually and via automation.Votes: 0GitHub stars: 9
- 299 Evaluation Results Bed1b9fcUnderstanding mcpbr evaluation results including resolution rates, JSON/YAML output formats, Markdown reports, and result comparison.Votes: 0GitHub stars: 9
- 312 Create Pr 2a980089Create PR as draft, wait for CI to pass, then mark ready for review (solves the "I'll check back later" problem)Votes: 0GitHub stars: 9
- 312 Create Pr 36af29d3Create pull request with optional contextVotes: 0GitHub stars: 9