Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add YuliaNuzhnenko/bioinformatics-agent-skills --skill tcga-cibersort-deconvgit clone --depth 1 https://github.com/YuliaNuzhnenko/bioinformatics-agent-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/yulianuzhnenko/bioinformatics-agent-skills/tcga-cibersort-deconv)<a href="https://agentmods.dev/skills/yulianuzhnenko/bioinformatics-agent-skills/tcga-cibersort-deconv"><img src="https://agentmods.dev/badge/skills/yulianuzhnenko/bioinformatics-agent-skills/tcga-cibersort-deconv/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/yulianuzhnenko/bioinformatics-agent-skills/tcga-cibersort-deconv"><img src="https://agentmods.dev/badge/skills/yulianuzhnenko/bioinformatics-agent-skills/tcga-cibersort-deconv.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00050 | $0.00468 |
| Opus 5 | $0.00025 | $0.00234 |
| Sonnet 5 | $0.00010 | $0.00094 |
| Haiku 4.5 | $0.00005 | $0.00047 |
Grade A, and why
tcga-cibersort-deconv scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
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.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 12d ago First seen · 55 lines · 50 tokens per session scan A 40ab49c2787c
tcga-cibersort-deconv is a skill published in the GitHub repository YuliaNuzhnenko/bioinformatics-agent-skills (9 stars, last pushed 1mo ago), licensed MIT. It adds 50 tokens to every session and 468 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other skills, from other repositories
imaging-data-commons
Query and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC collections, cancer imaging datasets, DICOM data access, radiology (CT, MR, PET) or pathology AI training sets, metadata queries, visualization, or license checks — even when the user doesn't explicitly…
genomic-intelligence
Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights. Six tasks over a REST API and a hosted MCP server (keyless public demo): promoter regions, splice donor/acceptor sites, enhancer…
lab-hardware-cad
Design custom laboratory hardware as parametric build123d models and export fabrication-ready STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mounts and breadboard adapters, cuvette and microplate holders, tube racks, animal-behavior rigs, and 3D-printed instrument fixtures. Use when a research…
pkpd-modeling
Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring. Use when…
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
statistical-analysis
Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting. Use whenever a user wants to compare groups, test a hypothesis, analyze experimental or survey data, check statistical assumptions, compute required…