YuliaNuzhnenko Agent Skill: TCGA Immune Microenvironment Deconvolution Skill
📌 Description
Downloads TCGA RNA-Seq datasets via TCGAbiolinks, normalizes log2(TPM+1) counts, and calculates tumor-infiltrating immune cell fractions (CIBERSORT).
🤖 Agent Execution Protocol
When an AI Agent is tasked with tcga-cibersort-deconv:
- Input Validation: Verify that the required input files or coordinates are supplied.
- Environment Check: Ensure dependencies (
TCGAbiolinks, limma, CIBERSORT, ggplot2) are installed. - Execution: Run the protocol pipeline snippet below.
- Output Generation: Produce actionable Markdown/JSON summaries with publication figures.
💻 Protocol Code Snippet
library(TCGAbiolinks)
query <- GDCquery(project="TCGA-LUAD", data.category="Transcriptome Profiling", data.type="Gene Expression Quantification")
📥 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.
📄 License
Distributed under the MIT License. See LICENSE for details.