Locusviz
D 60 completed
Other
unknown / r · small
94
Files
4,275
LOC
0
Frameworks
4
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Pipeline State
completedRun ID
#1526247Phase
doneProgress
0%Started
2026-04-16 14:28:20Finished
2026-04-16 14:28:20LLM tokens
0Pipeline Metadata
Stage
SkippedDecision
skip_scaffold_dupNovelty
17.27Framework unique
—Isolation
—Last stage change
2026-04-16 18:15:42Deduplication group #47862
Member of a group with 185 similar repo(s) — canonical #1559941 view group →
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AI Prompt
Create an R package called 'locusviz' for generating publication-quality, LocusZoom-style visualizations of GWAS data. The tool needs to support multi-panel plots combining Manhattan plots, fine-mapping results, LD patterns, and gene tracks. I need functions to handle flexible data input for GWAS summary statistics and fine-mapping outputs, while supporting both hg19 and hg38 genome builds. Key functions should include `plot_locuszoom()`, `plot_manhattan_panel()`, and `plot_fm_panel()`. Also include data processing utilities like `preprocess()` and `liftover_variant()` to standardize the input data.
r gwas visualization bioinformatics ggplot2 locuszoom genomics statistics r-package
Generated by gemma4:latest
Catalog Information
Create an R package called 'locusviz' for generating publication-quality, LocusZoom-style visualizations of GWAS data. The tool needs to support multi-panel plots combining Manhattan plots, fine-mapping results, LD patterns, and gene tracks. I need functions to handle flexible data input for GWAS summary statistics and fine-mapping outputs, while supporting both hg19 and hg38 genome builds. Key functions should include plot_locuszoom(), plot_manhattan_panel(), and plot_fm_panel(). Also inc
Tags
r gwas visualization bioinformatics ggplot2 locuszoom genomics statistics r-package
Quality Score
D
59.8/100
Structure
55
Code Quality
67
Documentation
55
Testing
15
Practices
78
Security
100
Dependencies
70
Strengths
- CI/CD pipeline configured (github_actions)
- Consistent naming conventions (snake_case)
- Good security practices — no major issues detected
- Properly licensed project
Weaknesses
- No tests found — high risk of regressions
- 299 duplicate lines detected — consider DRY refactoring
Recommendations
- Add a test suite — start with critical path integration tests
- Add a linter configuration to enforce code style consistency
Languages
Frameworks
None detected
Symbols
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function1
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