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SKILL verified MIT Self-run

Tcga Cibersort Deconv

skill-yulianuzhnenko-bioinformatics-agent-skills-tcga-cibersort-deconv · by YuliaNuzhnenko

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

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Install

$ agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-tcga-cibersort-deconv

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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● 3d ago

Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

Preview Execution monitoring

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About

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:

  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.

💻 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.

Source & license

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

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

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Versions

  • v0.1.0 Imported from the upstream source.

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