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 single-cell-chromatin-data-handlinggit 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/single-cell-chromatin-data-handling)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/single-cell-chromatin-data-handling"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/single-cell-chromatin-data-handling/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/single-cell-chromatin-data-handling"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/single-cell-chromatin-data-handling.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 | $0.00062 | $0.01188 |
| Opus 5 | $0.00031 | $0.00594 |
| Sonnet 5 | $0.00012 | $0.00238 |
| Haiku 4.5 | $0.00006 | $0.00119 |
Grade A, and why
single-cell-chromatin-data-handling 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 — 93 lines — stays where its author put it; the contents beside it link to each section on GitHub.
single-cell-chromatin-data-handling
Summary
Export peak-by-cell matrices from ArchR processed scATAC-seq projects into formats compatible with trajectory analysis tools such as STREAM. This skill bridges chromatin accessibility data with downstream trajectory inference by standardizing matrix representation and format.
When to use
After calling peaks and annotating cells in an ArchR project, when you need to perform trajectory analysis using STREAM or other external tools that require a peak-by-cell matrix in a specific tabular format (CSV or TSV) rather than native ArchR objects.
When NOT to use
- Input data are already in STREAM-native format or another trajectory tool format; re-exporting will cause redundant processing.
- Peak calls have not yet been performed on the ArchR project; missing peak annotations will result in an empty or malformed matrix.
- Using trajectory tools other than STREAM that have native ArchR support (monocle3, Slingshot); ArchR provides direct integration functions for these.
Inputs
- ArchR project object (processed with peak calls and cell annotations)
- Peak-by-cell accessibility matrix (internal to ArchR project)
Outputs
- STREAM-compatible peak-by-cell matrix file (CSV or TSV format)
- Peak identifiers and cell barcodes in STREAM-expected tabular layout
How to apply
Load a processed ArchR project object containing peak calls and cell annotations. Call the exportPeakMatrixForSTREAM function on the ArchR project to generate a peak-by-cell matrix formatted for STREAM compatibility. Write the resulting matrix to a file in STREAM-compatible format (typically CSV or TSV). The function handles matrix transposition and formatting internally; the user need only specify the output file path. This enables seamless integration with trajectory analysis workflows while preserving the peak-cell accessibility patterns derived from scATAC-seq analysis.
Related tools
- ArchR (scATAC-seq processing, peak calling, and matrix export via exportPeakMatrixForSTREAM function) — https://github.com/GreenleafLab/ArchR
- STREAM (Trajectory analysis tool that accepts the exported peak matrix for cell state inference)
- R (Programming environment for executing ArchR functions and file I/O operations)
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 · 93 lines · 62 tokens per session scan A 0867e68ebcdf
single-cell-chromatin-data-handling is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 2d ago), licensed Apache-2.0. It adds 62 tokens to every session and 1,188 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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