# Tcga Cibersort Deconv

> Downloads TCGA RNA-Seq datasets via TCGAbiolinks, normalizes log2(TPM+1) counts, and calculates tumor-infiltrating immune cell fractions (CIBERSORT).

- **Type:** Skill
- **Install:** `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-tcga-cibersort-deconv`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [YuliaNuzhnenko](https://agentstack.voostack.com/s/yulianuzhnenko)
- **Installs:** 0
- **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [YuliaNuzhnenko](https://github.com/YuliaNuzhnenko)
- **Source:** https://github.com/YuliaNuzhnenko/bioinformatics-agent-skills/tree/main/skills/tcga-cibersort-deconv

## Install

```sh
agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-tcga-cibersort-deconv
```

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

## About

# Agent Skill: TCGA Immune Microenvironment Deconvolution Skill

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## 📌 Description
Downloads TCGA RNA-Seq datasets via TCGAbiolinks, normalizes log2(TPM+1) counts, and calculates tumor-infiltrating immune cell fractions (CIBERSORT).

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## 🤖 Agent Execution Protocol

When an AI Agent is tasked with `tcga-cibersort-deconv`:
1. **Input Validation**: Verify that the required input files or coordinates are supplied.
2. **Environment Check**: Ensure dependencies (`TCGAbiolinks, limma, CIBERSORT, ggplot2`) are installed.
3. **Execution**: Run the protocol pipeline snippet below.
4. **Output Generation**: Produce actionable Markdown/JSON summaries with publication figures.

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## 💻 Protocol Code Snippet

```python
library(TCGAbiolinks)
query <- GDCquery(project="TCGA-LUAD", data.category="Transcriptome Profiling", data.type="Gene Expression Quantification")

```

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## 📥 Input & Output Specifications

### Input Contract
* **Target Files**: Valid input data matching domain formats.
* **Parameters**: Quality thresholds and cutoffs.

### Output Contract
* **Results Table**: Structured summary dataframe or matrix.
* **Visualization**: Rendered SVG/PNG figures.

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## 📄 License
Distributed under the MIT License. See `LICENSE` for details.

## Source & license

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

- **Author:** [YuliaNuzhnenko](https://github.com/YuliaNuzhnenko)
- **Source:** [YuliaNuzhnenko/bioinformatics-agent-skills](https://github.com/YuliaNuzhnenko/bioinformatics-agent-skills)
- **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-yulianuzhnenko-bioinformatics-agent-skills-tcga-cibersort-deconv
- Seller: https://agentstack.voostack.com/s/yulianuzhnenko
- Browse the marketplace: https://agentstack.voostack.com/browse

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