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 TianGzlab/OmicsClaw --skill bulkrna-splicinggit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote 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/tiangzlab/omicsclaw/bulkrna-splicing)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/bulkrna-splicing"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/bulkrna-splicing.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 2 findings, up to high
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 →
- high Rogue Agent · line 3 Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
- medium analysis-evasion · line 1 Suspicious Unicode normalization or mixed-script contentFix: Review the flagged content for security risks. Ensure no credentials, secrets, or sensitive data are exposed.
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 | $0.00056 | $0.01018 |
| Opus 5 | $0.00028 | $0.00509 |
| Sonnet 5 | $0.00011 | $0.00204 |
| Haiku 4.5 | $0.00006 | $0.00102 |
Grade A, and why
bulkrna-splicing 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 8d 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 — 86 lines — stays where its author put it; the contents beside it link to each section on GitHub.
bulkrna-splicing
When to use
Run AFTER rMATS or SUPPA2 has produced its splicing-event table — this skill consumes that output (not raw alignments). Computes per-event ΔPSI (delta percent-spliced-in), flags events crossing significance and ΔPSI thresholds, and groups results by event type (SE / A3SS / A5SS / MXE / RI).
Inputs & Outputs
Inputs
- File types:
.csv
Outputs
tables/significant_events.csvtables/splicing_events.csvfigures/dpsi_distribution.pngfigures/event_type_distribution.pngfigures/volcano_splicing.pngreport.mdresult.json
Flow
- Load splicing event table. Hard-fail at
bulkrna_splicing.py:365,368on missing or invalid--input. - Validate the fixed input schema: must contain columns
event_type, gene, delta_psi, padj(bulkrna_splicing.py:153-155). No format detection — caller must pre-flatten rMATS / SUPPA2 output to this schema. - Filter by
--dpsi-cutoffAND--padj-cutoff. - Group by event type; render distribution + volcano + bar plots.
- Emit
tables/splicing_events.csv(full) +tables/significant_events.csv(filtered) + report.
Gotchas
- This skill consumes the SPLICING TABLE, not BAM or FASTQ. Run rMATS or SUPPA2 upstream and feed their output here. The wrapper does not perform splicing detection itself — feeding it BAM files raises a parser error or silently produces an empty result.
--dpsi-cutoffis the ABSOLUTE value of ΔPSI. Default0.1keeps events with|ΔPSI| ≥ 0.1, including both inclusion-up and inclusion-down. Set to0to keep all directionally significant events.- Input schema is fixed:
event_type, gene, delta_psi, padj(with optionalpvalueandevent_id). The script does NOT auto-detect rMATS vs SUPPA2 column conventions — if your input uses rMATS'sIncLevelDifference/FDRor SUPPA2'sdPSI/pvalnatively, rename columns first or the loader will silently drop your data. - Event-type breakdown depends on the upstream tool's classification. rMATS reports SE / A3SS / A5SS / MXE / RI as separate files; SUPPA2 uses an EVENT field. Concatenate / re-label these into a single
event_typecolumn before feeding the skill, or the breakdown bar chart under-counts.
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- 8d ago First seen · 86 lines · 56 tokens per session scan A d7c70181b20a
bulkrna-splicing is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 56 tokens to every session and 1,018 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 2026-08-30.
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