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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-geogit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-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/alterlab-ieu/alterlab-academic-skills/alterlab-geo)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-geo"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-geo/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/alterlab-ieu/alterlab-academic-skills/alterlab-geo"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-geo.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00155 | $0.02134 |
| Opus 5 | $0.00077 | $0.01067 |
| Sonnet 5 | $0.00031 | $0.00427 |
| Haiku 4.5 | $0.00015 | $0.00213 |
Grade A, and why
alterlab-geo scanned grade A with 1 finding 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 9d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
allowed-tools: Read WebFetch Bash(curl:*) Bash(uv:*) How it starts
The opening of the file, as written. The whole thing — 166 lines — stays where its author put it; the contents beside it link to each section on GitHub.
GEO Database
Overview
The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. It holds hundreds of thousands of studies (Series) and millions of samples from both array-based and sequence-based experiments. For current totals see the GEO browser at https://www.ncbi.nlm.nih.gov/geo/.
When to Use This Skill
Use this skill when searching for gene expression datasets, retrieving experimental data, downloading raw and processed files, querying expression profiles, or integrating GEO data into computational analysis workflows.
Core Workflow
- Search for relevant studies (E-utilities /
Bio.Entrez) → seereferences/searching.md. - Retrieve a series with GEOparse:
GEOparse.get_GEO(geo="GSE...", destdir="./data")→ seereferences/geoparse_usage.md. - Extract the expression matrix via
gse.pivot_samples('VALUE')(genes × samples). - Analyze — QC, differential expression, clustering, meta-analysis → see
references/expression_analysis.md.
For bulk downloads, skip GEOparse and pull files directly over FTP → see references/data_access.md.
GEO Data Organization
GEO organizes data hierarchically using different accession types:
- Series (GSE) — a complete experiment with related samples (e.g.
GSE123456). Largest organizational unit. Holds experimental design, samples, study info. - Sample (GSM) — a single experimental sample / biological replicate
(e.g.
GSM987654). Linked to platforms and series. - Platform (GPL) — the microarray or sequencing platform (e.g.
GPL570, Affymetrix Human Genome U133 Plus 2.0 Array). Shared across experiments. - DataSet (GDS) — curated, consistently-formatted collections (e.g.
GDS5678) processed for differential analysis. Ideal for quick comparative analyses, but the curated GDS set is legacy and no longer growing — most recent studies exist only as GSE Series, so prefer GSE for new work. - Profiles — gene-specific expression data linked to sequence features, queryable by gene name, cross-referenced to Entrez Gene.
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- 9d ago First seen · 166 lines · 155 tokens per session scan A b3b185048cd9
alterlab-geo is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 7d ago), licensed MIT. It adds 155 tokens to every session and 2,134 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
ob-hrm-scale-adaptor
A guide for adapting organisational behaviour and human-resources survey scales across languages and cultures. It covers permission checks, translation and back-translation, expert review, participant interviews, and tests of whether groups interpret the scale comparably.
r-spss-syntax-architect
A guide for turning research hypotheses into repeatable R or SPSS code for statistical analysis. It covers panel data, where the same companies or other units are observed over time, as well as interaction effects, curves, and mediation.
thesis-consistency-audit
A consistency audit for quantitative master’s and doctoral theses in management, finance, or strategy. It checks whether numbers, tables, analyses, and claims agree, and can inspect hidden author information in office documents.
management-figure
A chart-making toolkit for evidence-based management, finance, and strategy research. It creates publication-ready plots from regression results and tracking data, including coefficient, interaction, group-comparison, trend, and curved-relationship charts.
reproducibility-architect
A guide for packaging research so another person can rerun its data processing and analysis. A replication package is the project files, instructions, code, data guidance, and software details needed to reproduce published results.
journal-submission-scout
A research tool for choosing a journal for a completed paper. It searches for journals that publish similar work, compares public information such as citation data, fees, open-access listing, and review practices, and screens for warning signs of predatory journals, which charge authors without providing trustworthy publishing services.