Add comprehensive database exploration vignette #1
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- Create new vignette 'exploring-omicidx-database.qmd' with detailed examples - Demonstrate R6 Omicidx class usage across multiple query types - Include exploration of studies, experiments, samples, and runs tables - Add cross-table queries and advanced analysis examples - Update _pkgdown.yml to include new vignette in documentation - Organize vignettes into 'Getting Started' and 'Data Exploration' sections
- Correct column names (instrument_model, pubmed_ids) - Remove queries for non-existent columns (total_bases, total_spots) - Fix dbplyr compatibility issues (remove paste() with collapse) - Simplify cross-table joins to avoid suffix issues - Focus on metadata exploration rather than data volume statistics - All queries now successfully execute against the actual database
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Summary
This PR adds a comprehensive new vignette that demonstrates how to explore and query the OmicIDX DuckDB database using the
OmicidxR6 class.Changes
exploring-omicidx-database.qmd- A detailed guide with extensive query examples_pkgdown.ymlto organize vignettes into logical sectionsVignette Contents
The new vignette provides a structured exploration of the database with sections covering:
Basic Operations
Entity-Specific Exploration (H3 sections)
Advanced Analysis
Benefits
Testing
The vignette uses standard dplyr and DBI operations that work with the existing
OmicidxR6 class. All queries follow best practices for lazy evaluation and efficient data retrieval.Documentation
The vignette is properly integrated into pkgdown documentation with a dedicated "Data Exploration" section.