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 methylation-object-merging-and-uniongit 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/methylation-object-merging-and-union)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/methylation-object-merging-and-union"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/methylation-object-merging-and-union/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/methylation-object-merging-and-union"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/methylation-object-merging-and-union.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 | $0.00050 | $0.01256 |
| Opus 5 | $0.00025 | $0.00628 |
| Sonnet 5 | $0.00010 | $0.00251 |
| Haiku 4.5 | $0.00005 | $0.00126 |
Grade A, and why
methylation-object-merging-and-union 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 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.
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 — 93 lines — stays where its author put it; the contents beside it link to each section on GitHub.
methylation-object-merging-and-union
Summary
Merge methylation call objects across multiple bisulfite sequencing samples to create a unified methylBase object containing only bases with coverage in all samples. This is a prerequisite for comparative differential methylation analysis, ensuring consistent base-pair resolution across the sample cohort.
When to use
You have loaded individual methylation call files as methylRawList objects from bisulfite sequencing experiments (via methRead()) and need to perform base-level comparative analysis across two or more samples. The goal is to identify a common set of covered loci before calculating differential methylation statistics.
When NOT to use
- Input is already a methylBase object; merging is not needed.
- You wish to perform single-sample methylation statistics or visualization without cross-sample comparison.
- Coverage is highly uneven across samples and you prefer to use coverage-weighted or missing-data-imputation strategies instead of complete-case deletion.
Inputs
- methylRawList object (collection of methylRaw objects, one per sample, from methRead())
- Methylation call files in text format with per-base cytosine calls
Outputs
- methylBase object (merged methylation matrix with bases covered in all samples)
How to apply
Apply the unite() function to a methylRawList object to merge all samples and retain only those base-pair locations covered in every sample in the cohort. The resulting methylBase object contains a consistent set of bases suitable for downstream statistical testing via calculateDiffMeth(). This union operation is essential because differential methylation analysis requires paired observations across all samples; bases missing in even one sample are excluded. The merger also standardizes the coverage landscape, reducing heterogeneity that would inflate false positives in Fisher's exact test or logistic regression.
Related tools
- methylKit (R package providing methRead() and unite() functions for loading and merging methylation call objects) — https://github.com/al2na/methylKit
- Bismark (Bisulfite alignment and methylation calling tool producing input call files for methRead()) — https://github.com/FelixKrueger/Bismark
- MethylDackel (Alternative tool for extracting per-base methylation metrics from BAM/CRAM files, producing input-compatible call files) — https://github.com/dpryan79/MethylDackel
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 · 93 lines · 50 tokens per session scan A aba5f1f36551
methylation-object-merging-and-union is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 2d ago), licensed Apache-2.0. It adds 50 tokens to every session and 1,256 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 2026-09-03.
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