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 cis-contact-frequency-analysisgit 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/cis-contact-frequency-analysis)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/cis-contact-frequency-analysis"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/cis-contact-frequency-analysis/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/cis-contact-frequency-analysis"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/cis-contact-frequency-analysis.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 | $0.00036 | $0.01329 |
| Opus 5 | $0.00018 | $0.00665 |
| Sonnet 5 | $0.00007 | $0.00266 |
| Haiku 4.5 | $0.00004 | $0.00133 |
Grade A, and why
cis-contact-frequency-analysis 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 11d 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 — 99 lines — stays where its author put it; the contents beside it link to each section on GitHub.
cis-contact-frequency-analysis
Summary
Compute and analyze contact frequency as a function of genomic distance within the same chromosome (cis contacts) using cooler-formatted Hi-C matrices. This is a foundational Hi-C analysis that reveals the prominent distance-dependent decay of chromatin contacts.
When to use
When you have loaded a cooler file containing Hi-C contact matrices and need to quantify how contact probability decays with genomic distance within a single chromosome. This is typically one of the first analyses performed on Hi-C data to characterize the global organizational properties of chromatin and to validate data quality before proceeding to domain-level or structural feature detection.
When NOT to use
- Input cooler file is already filtered, normalized, and pre-computed contact frequency tables exist — use those directly instead of recalculating.
- Trans (inter-chromosomal) contact analysis is the primary goal — this skill is specific to cis contacts within a single chromosome.
- You need to detect specific chromatin structures (TADs, loops, compartments) rather than global distance-decay properties — use domain-detection or loop-calling methods instead.
Inputs
- cooler file (.cool or .mcool) containing Hi-C contact matrix
- target chromosome identifier
- genomic distance binning specification (bin size in base pairs)
Outputs
- distance-binned contact frequency table (CSV/TSV with genomic separation and contact counts)
- P(s) curve (contact probability vs. genomic distance)
- visualization (log–log plot of contact frequency vs. distance)
How to apply
Load the cooler file using the cooler library and extract the contact matrix for a target chromosome. Use cooltools functions to compute per-bin sequencing depth (coverage) to normalize for bias, then aggregate contacts across genomic distance bins (e.g., 1 kb, 5 kb, 10 kb bins) to produce a distance-binned contact frequency vector. Optionally compute the P(s) curve (probability of contact as a function of separation distance s) and smooth it to reduce noise. Export the results as a tabular format (CSV/TSV) with bin coordinates and normalized contact counts, and visualize as a log–log plot to assess the power-law decay characteristic of polymer-like chromatin behavior.
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.
- 11d ago First seen · 99 lines · 36 tokens per session scan A 1c01732a5485
cis-contact-frequency-analysis is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 5d ago), licensed Apache-2.0. It adds 36 tokens to every session and 1,329 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 2026-08-30.
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