# Tcga Cibersort Deconv

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

- Skill: `yulianuzhnenko/tcga-cibersort-deconv` (Agent Skill)
- Install (CLI): `npx skillmds@latest add yulianuzhnenko/tcga-cibersort-deconv`
- Raw SKILL.md: https://api.skillmd.com/api/skills/yulianuzhnenko/tcga-cibersort-deconv/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: YuliaNuzhnenko (https://skillmd.com/u/yulianuzhnenko)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/yulianuzhnenko/tcga-cibersort-deconv

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# Agent Skill: TCGA Immune Microenvironment Deconvolution Skill

[![Domain](https://img.shields.io/badge/Domain-Cancer%20Genomics-00f0ff?style=flat-square)](#)
[![Version](https://img.shields.io/badge/Version-1.0.0-green?style=flat-square)](#)

## 📌 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.