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- 572 Usage Guide F277565fCNVkit 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.Votes: 0GitHub stars: 9
- 572 Usage Guide F5a6c034Convert between different gene identifier systems (Ensembl, Symbol, Entrez, UniProt) using mygene, biomaRt, and org.db packages for cross-database integration.Votes: 0GitHub stars: 9
- 572 Usage Guide F65c534fDetect differential alternative splicing between experimental conditions. Identifies splicing events that change significantly between groups, reporting both statistical significance and effect size (delta PSI).Votes: 0GitHub stars: 9
- 572 Usage Guide F7c88fd3MOFA2 (Multi-Omics Factor Analysis v2) is an unsupervised method for integrating multiple omics layers. It decomposes the data into latent factors that explain shared and view-specific variation.Votes: 0GitHub stars: 9
- 572 Usage Guide F8d67e68Clustered heatmaps visualize matrix data (expression, methylation, etc.) with hierarchical clustering to reveal patterns across samples and features.Votes: 0GitHub stars: 9
- 572 Usage Guide F9cff9cfAssess ATAC-seq library quality using TSS enrichment, FRiP scores, fragment size distributions, mitochondrial contamination, and library complexity metrics.Votes: 0GitHub stars: 9
- 572 Usage Guide Fa1902d2Pathway mapping places differential metabolites in biological context, identifying affected metabolic processes using enrichment analysis and pathway topology.Votes: 0GitHub stars: 9
- 572 Usage Guide Fcc82e24Build classification models for biomarker discovery and diagnostics using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs.Votes: 0GitHub stars: 9
- 573 Python 312 560b9cd0This document provides complete, canonical type annotation guidance for Python 3.12.Votes: 0GitHub stars: 9
- 600 Reference 080807b8- [CloudWatch Resources](#cloudwatch-resources) - [Common Properties](#common-properties) - [Alarm Configuration](#alarm-configuration) - [Dashboard Widgets](#dashboard-widgets) - [Log Group Configuration](#log-group-configuration) - [Metric Properties](#metric-properties)Votes: 0GitHub stars: 9
- 600 Reference 09e4bad6详细的 pandas 和 openpyxl API 参考指南Votes: 0GitHub stars: 9
- 600 Reference 4ec85722This is the full reference documentation for the Github agent connector.Votes: 0GitHub stars: 9
- 600 Reference 5899aaeaThis is the full reference documentation for the Google-Analytics-Data-Api agent connector.Votes: 0GitHub stars: 9
- 600 Reference 5c30fc8b```typescript 'use server';Votes: 0GitHub stars: 9
- 600 Reference 7ea57731This is the full reference documentation for the Linear agent connector.Votes: 0GitHub stars: 9
- 600 Reference 87a2fde71. Go to [Google AI Studio](https://aistudio.google.com/) 2. Click "Get API Key" 3. Create a new API key or use an existing oneVotes: 0GitHub stars: 9
- 600 Reference 8a31fccaThis is the full reference documentation for the Linear agent connector.Votes: 0GitHub stars: 9
- 600 Reference Cdceae16This is the full reference documentation for the Linear agent connector.Votes: 0GitHub stars: 9
- 600 Reference Dfcc13b3This is the full reference documentation for the Github agent connector.Votes: 0GitHub stars: 9
- 600 Reference Fe842b1bThis is the full reference documentation for the Github agent connector.Votes: 0GitHub stars: 9
- 602 Transactions 5321f762Monitor database transactions with real-time alerting for performance and...Votes: 0GitHub stars: 9
- 602 Transactions 84ce85e7Monitor database transactions with real-time alerting for performance and lock issuesVotes: 0GitHub stars: 9
- 607 Best Practices 3fc17cd6```bash release: "myapp@1.2.3" release: "myapp@abc123"Votes: 0GitHub stars: 9
- 607 Best Practices 47bcc05b<!-- START doctoc generated TOC please keep comment here to allow auto update --> <!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE --> **Table of Contents** *generated with [DocToc](https://github.com/thlorenz/doctoc)*Votes: 0GitHub stars: 9
- 607 Best Practices 56df858d**Airflow 2.x:** ```python from airflow.decorators import dag, task, task_group, setup, teardown from airflow.models import Variable from airflow.hooks.base import BaseHook ```Votes: 0GitHub stars: 9
- 607 Best Practices Ab33237f<!-- START doctoc generated TOC please keep comment here to allow auto update --> <!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE --> **Table of Contents** *generated with [DocToc](https://github.com/thlorenz/doctoc)*Votes: 0GitHub stars: 9
- 626 Analytics Dashboard Bfad4f5bThe Local Deep Research metrics dashboard provides insights into your research activities, costs, and system performance. > **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
- 627 Library And Rag 6ebbccebThis guide covers the Research Library for document management and the RAG (Retrieval-Augmented Generation) system for semantic search.Votes: 0GitHub stars: 9
- 628 Dashboard Improvements 1ea6e4a3The metrics dashboard now provides comprehensive analytics with:Votes: 0GitHub stars: 9
- 647 04 Frontend Challenge 02d8e8f5Build beautiful, functional interfaces for AI agent management! This challenge is for frontend engineers who want to contribute to Honeycomb, Aden's dashboard. **Difficulty:** Intermediate **Time:** 1-2 hours **Prerequisites:** Complete [Getting Started](./01-getting-started.md), React/TypeScript experience ---Votes: 0GitHub stars: 9
- 653 New Categories Plan 32dc579f1. **alternative-splicing** - Isoform and splicing analysis 2. **chemoinformatics** - Small molecule and drug discovery 3. **liquid-biopsy** - cfDNA and circulating tumor DNA analysisVotes: 0GitHub stars: 9
- 654 Plugin Assessor 57be0dc6Analyze Claude Code plugins for structural correctness, frontmatter optimization, schema compliance, and enhancement opportunities. Use when reviewing plugins before marketplace submission, auditing existing plugins, validating plugin structure, or identifying improvements. Handles large plugins with many reference files. Detects orphaned documentation, duplicate content, and missing cross-references.Votes: 0GitHub stars: 9
- 654 Plugin Assessor C3bafbafAnalyze Claude Code plugins for structural correctness, frontmatter optimization, schema compliance, and enhancement opportunities. Use when reviewing plugins before marketplace submission, auditing existing plugins, validating plugin structure, or identifying improvements. Handles large plugins with many reference files. Detects orphaned documentation, duplicate content, and missing cross-references.Votes: 0GitHub stars: 9
- 654 Plugin Assessor E8cff6b6Analyze Claude Code plugins for structural correctness, frontmatter optimization, schema compliance, and enhancement opportunities. Use when reviewing plugins before marketplace submission, auditing existing plugins, validating plugin structure, or identifying improvements. Handles large plugins with many reference files. Detects orphaned documentation, duplicate content, and missing cross-references.Votes: 0GitHub stars: 9
- 655 Write To Skill File 4ed508c4Text to LLM Optimized Text workflow instructionsVotes: 0GitHub stars: 9
- 655 Write To Skill File 6969482eText to LLM Optimized Text workflow instructionsVotes: 0GitHub stars: 9
- 656 Plannotator 931bcc12| Field | Value | | ------------- | ----------------------------------------------- | | Research Date | 2026-01-31 | | Primary URL | <https://plannotator.ai> | | GitHub | <https://github.com/backnotprop/plannotator> | | Version | No formal releases (monorepo, continuous dev) | | License | BSL 1.1 (Business Source License) | | Created | 202...Votes: 0GitHub stars: 9
- 657 Repomix 89f4aa7b**Research Date**: January 31, 2026 **Source URL**: <https://repomix.com> **GitHub Repository**: <https://github.com/yamadashy/repomix> **npm Package**: <https://www.npmjs.com/package/repomix> **Version at Research**: v1.11.1 **License**: MIT ---Votes: 0GitHub stars: 9
- 658 Hallucination Triggers 2f73b363This guide catalogs observable triggers that indicate reasoning failures in AI agent outputs, particularly when orchestrating AI-to-AI delegation. These triggers reveal when agents generate conventional-looking outputs through pattern-matching rather than reasoning about actual problem requirements.Votes: 0GitHub stars: 9
- 658 Hallucination Triggers A1b557adThis guide catalogs observable triggers that indicate reasoning failures in AI agent outputs, particularly when orchestrating AI-to-AI delegation. These triggers reveal when agents generate conventional-looking outputs through pattern-matching rather than reasoning about actual problem requirements.Votes: 0GitHub stars: 9
- 659 Description Skill 12d2045cSummarize files by reading content, extracting key passages, and applying type-specific strategies. Activates on summarize this file, what's in this file, describe this codebase, file summary, analyze this file, tl;dr this file, what does this code do, explain this config, break down this script. Routes to strategies for code, config, data, documentation, markup, and binary files based on extension and word count.Votes: 0GitHub stars: 9
- 659 Description Skill 141ea578Orchestrates specialized agents to create high-quality Claude Code plugins. Delegates to researcher agents for domain knowledge, Explore agents for code discovery, validation agents for official docs verification, and review agents for quality checks. Use when creating new plugins or improving existing ones.Votes: 0GitHub stars: 9
- 659 Description Skill 20d35095Add resources to the research directory with comprehensive documentation. Supports single URL, batch processing via --batch, re-research via --rerun, and validation via --validate. Triggers on "add to research", "document this tool", "research this", or URLs to novel agentic development resources.Votes: 0GitHub stars: 9
- 659 Description Skill 34e26edcDescribe images and screenshots by viewing content with multimodal Read tool and documenting only visible elements. Activates on what's in this image, describe this screenshot, summarize this diagram, image summary, what does this screenshot show, explain this diagram, break down this chart. Handles UI screenshots, architecture diagrams, charts, photos, code screenshots, and terminal output. Never infers from filenames.Votes: 0GitHub stars: 9
- 659 Description Skill 40b7921eSAM Stage 5 — Stateless execution of a single task in a fresh agent session. The task file IS the complete prompt containing all context needed. Used when dispatching a task to an agent; produces the EXECUTION artifact with implementation results and verification output.Votes: 0GitHub stars: 9
- 659 Description Skill 6b040a2bTransform transcript analysis findings into actionable improvements. Triggers on "generate hooks from findings", "improve agent", "fix anti-pattern", "kaizen improvement", "generate hook proposals", or "create improvement plan". Provides templates for hook generation, agent prompt refinement, skill patches, CLAUDE.md updates, and script automation from analysis data.Votes: 0GitHub stars: 9
- 659 Description Skill 7137a36fOrchestrates specialized agents to create high-quality Claude Code plugins. Delegates to researcher agents for domain knowledge, Explore agents for code discovery, validation agents for official docs verification, and review agents for quality checks. Use when creating new plugins or improving existing ones.Votes: 0GitHub stars: 9
- 659 Description Skill 72eabf07Add resources to the research directory with comprehensive documentation. Supports single URL, batch processing via --batch, re-research via --rerun, and validation via --validate. Triggers on "add to research", "document this tool", "research this", or URLs to novel agentic development resources.Votes: 0GitHub stars: 9
- 659 Description Skill 7b8e23d4Audit skill lifecycle by tracing call chains, detecting circular dependencies, finding instruction contradictions, identifying duplicated datasets, analyzing bidirectional coherence, discovering scriptable sequences, and learning patterns. Use when checking skill coherence, validating skill workflow, finding semantic gaps in plugin structure, or auditing plugin before marketplace submission. Generates audit reports to .claude/audits/ with findings by dimension.Votes: 0GitHub stars: 9
- 659 Description Skill A62feeb1SAM Stage 5 — Stateless execution of a single task in a fresh agent session. The task file IS the complete prompt containing all context needed. Used when dispatching a task to an agent; produces the EXECUTION artifact with implementation results and verification output.Votes: 0GitHub stars: 9