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 scatac-seq-peak-matrix-exportgit 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/scatac-seq-peak-matrix-export)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/scatac-seq-peak-matrix-export"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/scatac-seq-peak-matrix-export/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/scatac-seq-peak-matrix-export"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/scatac-seq-peak-matrix-export.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 Output Handling · line 79 Output size or generation rate is not bounded. Unbounded output enables denial-of-service through resource exhaustion, log flooding, or context-window stuffing.Fix: Set explicit limits on output length, generation count, and rate. Use max_tokens and truncation to prevent unbounded output.
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 | $0.00066 | $0.01285 |
| Opus 5 | $0.00033 | $0.00642 |
| Sonnet 5 | $0.00013 | $0.00257 |
| Haiku 4.5 | $0.00007 | $0.00128 |
Grade A, and why
scatac-seq-peak-matrix-export 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 — 97 lines — stays where its author put it; the contents beside it link to each section on GitHub.
scatac-seq-peak-matrix-export
Summary
Export a peak-by-cell accessibility matrix from a processed ArchR project into STREAM-compatible format for downstream trajectory analysis. This skill bridges scATAC-seq peak quantification and external trajectory inference tools.
When to use
After completing peak calling and cell annotation in an ArchR project, when you intend to perform trajectory analysis using STREAM rather than ArchR's native monocle3 or Slingshot integrations, or when you need to share peak-by-cell matrices with collaborators using STREAM pipelines.
When NOT to use
- Your downstream analysis uses monocle3 or Slingshot, which ArchR directly supports via addMonocleTrajectory or addSlingShotTrajectories without intermediate export.
- You require gene expression matrices rather than chromatin accessibility; use addGeneExpressionMatrix instead.
- Your peak matrix has already been exported or you are working with pre-computed accessibility matrices from external sources.
Inputs
- ArchR project object (containing peak calls and cell annotations)
- Cell metadata with trajectory or treatment information
Outputs
- Peak-by-cell matrix in STREAM-compatible format (CSV or TSV)
- Matrix with peaks as rows and cells as columns
How to apply
Load a processed ArchR project object containing peak calls and cell metadata annotations. Call the exportPeakMatrixForSTREAM function on the ArchR project to generate a peak-by-cell matrix formatted for STREAM compatibility. The function outputs a matrix where rows represent peaks (genomic loci) and columns represent single cells, with binary or continuous accessibility values. Write the resulting matrix to a file in STREAM-compatible format (typically CSV or TSV). Verify the output matrix dimensions match your expected peak and cell counts, and confirm the file format matches STREAM's input requirements.
Related tools
- ArchR (Primary R package for scATAC-seq processing; provides the exportPeakMatrixForSTREAM function to generate STREAM-compatible peak matrices.) — https://github.com/GreenleafLab/ArchR
- STREAM (Downstream trajectory analysis tool that accepts peak-by-cell matrices exported from ArchR.)
- monocle3 (Alternative trajectory analysis tool directly supported by ArchR; use if STREAM export is not needed.)
- Slingshot (Alternative trajectory analysis tool directly supported by ArchR; use if STREAM export is not needed.)
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 · 97 lines · 66 tokens per session scan A 1f03d6ac964d
scatac-seq-peak-matrix-export is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 2d ago), licensed Apache-2.0. It adds 66 tokens to every session and 1,285 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 2026-09-06.
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