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 HolobiomicsLab/asb-skill-collections --skill probe-detection-pvalue-filteringgit clone --depth 1 https://github.com/HolobiomicsLab/asb-skill-collectionsWrote 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/holobiomicslab/asb-skill-collections/probe-detection-pvalue-filtering)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/probe-detection-pvalue-filtering"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/probe-detection-pvalue-filtering/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/holobiomicslab/asb-skill-collections/probe-detection-pvalue-filtering"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/probe-detection-pvalue-filtering.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Excessive Agency · line 60 Skill enables autonomous high-impact decisions without human-in-the-loop verification. Critical operations (destructive commands, financial transactions, data deletion) should require explicit user confirmation.Fix: Add human-in-the-loop confirmation for destructive, irreversible, or high-impact operations. Never auto-execute commands that modify files, send data, or alter system state.
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 | $0.00048 | $0.01359 |
| Opus 5 | $0.00024 | $0.00679 |
| Sonnet 5 | $0.00010 | $0.00272 |
| Haiku 4.5 | $0.00005 | $0.00136 |
Grade A, and why
probe-detection-pvalue-filtering 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 6d 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.
How it starts
The opening of the file, as written. The whole thing — 96 lines — stays where its author put it; the contents beside it link to each section on GitHub.
probe-detection-pvalue-filtering
Summary
Remove low-quality DNA methylation probes by filtering out those with detection p-value > 0.01 using ChAMP's default filtering function. This is a standard quality-control step applied early in the 450k and EPIC array analysis pipeline to exclude probes with unreliable signal intensity measurements.
When to use
Apply this skill immediately after loading raw methylation array data (.idat files or beta-valued matrix) from HumanMethylation450 (450k) or EPIC arrays when conducting primary quality control. Use it before normalization, type-2 probe correction, or downstream statistical analysis to ensure that only probes with confident detection calls are carried forward.
When NOT to use
- Data has already undergone detection p-value filtering in an upstream pipeline
- Working with pre-filtered public datasets where probe quality has already been vetted
- Analysis requires retention of all probes, including low-confidence ones, for methodological reasons (e.g., benchmarking filtering algorithms themselves)
Inputs
- Raw methylation array data from HumanMethylation450 or EPIC arrays (.idat files)
- Beta-valued matrix (M-values or beta values) from methylation arrays
- Detection p-value matrix (one p-value per probe per sample)
Outputs
- Filtered probe matrix with low-confidence probes removed
- Pre- and post-filter probe count comparison
- Quality control report documenting filtering statistics
How to apply
Load your 450k or EPIC methylation array dataset using ChAMP's data import functions (from .idat files or beta-valued matrix). Apply champ.filter() with default parameters, which automatically removes probes with detection p-value > 0.01 in the first filtering step. This threshold reflects Illumina's standard confidence threshold for detected signal above background noise. Verify filtering success by comparing probe counts before and after filtering; probes with p-value > 0.01 should be absent from the post-filter matrix. Document the number of probes retained and removed in a quality control report for transparency and reproducibility.
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.
- 6d ago First seen · 96 lines · 48 tokens per session scan A 5c225d778f79
probe-detection-pvalue-filtering is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed yesterday), licensed Apache-2.0. It adds 48 tokens to every session and 1,359 once invoked, about $0.0002 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 2026-09-06.
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