investigate-great-rgreat

Metadata

Status	done
Assigned	`agent-81`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-04-01T14:48:32.355750163+00:00
Started	2026-04-01T14:50:32.970503368+00:00
Completed	2026-04-01T14:52:32.246041265+00:00
Tags	`eval-scheduled`
Eval score	0.87
└ blocking impact	0.85
└ completeness	0.95
└ coordination overhead	0.90
└ correctness	0.90
└ downstream usability	0.80
└ efficiency	0.85
└ intent fidelity	0.93
└ style adherence	0.90

Description

Goal

Investigate GREAT (Genomic Regions Enrichment of Annotations Tool) and rGREAT R package for region-based enrichment analysis that naturally handles multi-copy genes.

Specific Questions

Is rGREAT available as R package vs web tool only?
Does it work with CHM13 coordinates or only GRCh38?
Can we use 29 PHR BED intervals as input?
What background is appropriate (subtelomeric regions vs whole genome)?
What are computational requirements and expected runtime?

Output

Detailed assessment of GREAT/rGREAT feasibility
Installation/availability status
Input format requirements
Pros and cons for our specific use case
Runtime estimates

Validation

GREAT vs rGREAT availability confirmed
CHM13 coordinate compatibility checked
Input format documented with examples

## Goal
Investigate GREAT (Genomic Regions Enrichment of Annotations Tool) and rGREAT R package for region-based enrichment analysis that naturally handles multi-copy genes.

## Specific Questions
- Is rGREAT available as R package vs web tool only?
- Does it work with CHM13 coordinates or only GRCh38? 
- Can we use 29 PHR BED intervals as input?
- What background is appropriate (subtelomeric regions vs whole genome)?
- What are computational requirements and expected runtime?

## Output
- Detailed assessment of GREAT/rGREAT feasibility
- Installation/availability status
- Input format requirements
- Pros and cons for our specific use case
- Runtime estimates

## Validation  
- GREAT vs rGREAT availability confirmed
- CHM13 coordinate compatibility checked
- Input format documented with examples

Depends on

Required by

done synthesize-findings-and

Log

2026-04-01T14:50:32.970504461+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-01T14:50:58.451933691+00:00 Starting investigation of GREAT/rGREAT region-based enrichment tools
2026-04-01T14:52:15.503400556+00:00 Created comprehensive GREAT/rGREAT investigation report addressing all key questions
2026-04-01T14:52:29.292224573+00:00 Validated: all criteria met - availability confirmed, CHM13 compatibility assessed, input format documented with feasibility analysis
2026-04-01T14:52:32.246049451+00:00 Task marked as done