# Genomics Analysis

> Genomics analysis in R with Bioconductor, differential expression, enrichment, batch correction, and single-cell workflows.

- **Type:** Skill
- **Install:** `agentstack add skill-choxos-biostatagent-genomics-analysis`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [choxos](https://agentstack.voostack.com/s/choxos)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [choxos](https://github.com/choxos)
- **Source:** https://github.com/choxos/BiostatAgent/tree/main/plugins/r-tidy-modeling/skills/genomics-analysis

## Install

```sh
agentstack add skill-choxos-biostatagent-genomics-analysis
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Genomics Analysis in R

## Overview

Comprehensive genomics and bioinformatics statistical methods using Bioconductor packages. Covers differential expression analysis, pathway enrichment, and visualization for RNA-seq and microarray data.

## Bioconductor Setup

```r
# Install Bioconductor
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# Install packages
BiocManager::install(c(
  "DESeq2",
  "edgeR",
  "limma",
  "clusterProfiler",
  "org.Hs.eg.db",
  "EnhancedVolcano",
  "ComplexHeatmap"
))
```

## RNA-seq Differential Expression

### DESeq2 Analysis

```r
library(DESeq2)

# Create DESeqDataSet from count matrix
dds = 10) >= min_samples
dds  1)
```

### DESeq2 with Multiple Factors

```r
# Multi-factor design
dds  1))

# Convert to Entrez IDs
gene_ids  200 &
                              nFeature_RNA < 5000 &
                              percent.mt < 20)

# Normalize
seurat_obj <- NormalizeData(seurat_obj)
seurat_obj <- FindVariableFeatures(seurat_obj, nfeatures = 2000)

# Scale and PCA
seurat_obj <- ScaleData(seurat_obj)
seurat_obj <- RunPCA(seurat_obj)

# Clustering
seurat_obj <- FindNeighbors(seurat_obj, dims = 1:20)
seurat_obj <- FindClusters(seurat_obj, resolution = 0.5)

# UMAP
seurat_obj <- RunUMAP(seurat_obj, dims = 1:20)
DimPlot(seurat_obj, reduction = "umap")

# Find markers
markers <- FindAllMarkers(seurat_obj, only.pos = TRUE)
```

## GWAS Analysis

### Basic Association Testing

```r
# Simple association test
gwas_results <- apply(genotype_matrix, 2, function(snp) {
  fit <- glm(phenotype ~ snp + covariates, family = binomial)
  summary(fit)$coefficients["snp", ]
})

# Manhattan plot
library(qqman)
manhattan(gwas_results, chr = "CHR", bp = "BP", p = "P", snp = "SNP")
qq(gwas_results$P)
```

## Key Packages Summary

| Package | Purpose |
|---------|---------|
| DESeq2 | RNA-seq differential expression |
| edgeR | RNA-seq analysis |
| limma | Microarray and RNA-seq |
| clusterProfiler | Pathway analysis |
| EnhancedVolcano | Volcano plots |
| ComplexHeatmap | Advanced heatmaps |
| Seurat | Single-cell RNA-seq |
| sva | Batch correction |
| qqman | GWAS visualization |

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [choxos](https://github.com/choxos)
- **Source:** [choxos/BiostatAgent](https://github.com/choxos/BiostatAgent)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-choxos-biostatagent-genomics-analysis
- Seller: https://agentstack.voostack.com/s/choxos
- Browse the marketplace: https://agentstack.voostack.com/browse

---
Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.