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bio-data-visualization-upset-plots
library(UpSetR) upset(fromExpression(data), order.by = 'freq', nsets = 6) genesets <- list( SetA = c('Gene1', 'Gene2', 'Gene3', 'Gene4'), SetB = c('Ge...
requesting-code-review
Dispatch superpowers:code-reviewer subagent to catch issues before they cascade. Core principle: Review early, review often. Mandatory: After each tas...
bio-data-visualization-circos-plots
Circular genome visualizations for displaying multiple data tracks around chromosome ideograms. | Tool | Language | Best For | |------|----------|----...
bio-rna-quantification-featurecounts-counting
Count reads mapping to genomic features (genes, exons) from BAM files. featureCounts -a annotation.gtf -o counts.txt aligned.bam featureCounts -a anno...
bio-batch-processing
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pac...
alphafold
| Requirement | Minimum | Recommended | |-------------|---------|-------------| | Python | 3.8+ | 3.10 | | CUDA | 11.0+ | 12.0+ | | GPU VRAM | 32GB | ...
ontology-explorer
Enable an agent to understand, navigate, and query the structure of materials science ontologies without loading verbose OWL/XML files directly. Provi...
bio-chipseq-differential-binding
Reference examples tested with: DESeq2 1.42+, edgeR 4.0+ Before using code patterns, verify installed versions match. If versions differ: R: packageVe...
bio-workflows-scrnaseq-pipeline
Complete workflow from 10X Genomics Cell Ranger output to annotated cell types. 10X data (filteredfeaturebcmatrix) [1. Load Data] ---------> Read10X /...
pdx-model-analysis-agent
The PDX Model Analysis Agent provides AI-driven analysis of patient-derived xenograft models for preclinical drug testing, translational research, and...
bio-gatk-variant-calling
Reference examples tested with: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: CLI: <tool>...
chemical-property-lookup
description (10-20 chars): RDKit stats keywords: SMILES, RDKit, Lipinski, QED, ADMET measurableoutcome: Return a validated property summary (JSON + Li...