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-geneid-mappinggit 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-geneid-mapping)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/bulkrna-geneid-mapping"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/bulkrna-geneid-mapping/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/tiangzlab/omicsclaw/bulkrna-geneid-mapping"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/bulkrna-geneid-mapping.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, 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.
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 | $0.00059 | $0.01096 |
| Opus 5 | $0.00030 | $0.00548 |
| Sonnet 5 | $0.00012 | $0.00219 |
| Haiku 4.5 | $0.00006 | $0.00110 |
Grade A, and why
bulkrna-geneid-mapping 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 10d 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 — 88 lines — stays where its author put it; the contents beside it link to each section on GitHub.
bulkrna-geneid-mapping
When to use
Run between counting and downstream analysis when the gene identifiers
in your count matrix don't match the namespace of your downstream tool
(e.g. STARsolo gives Ensembl IDs but GSEA wants HGNC symbols).
Currently supports Ensembl ↔ Entrez ↔ HGNC symbol for human and mouse
via built-in tables, with optional mygene API enrichment. UniProt is
not supported — feed via --mapping-file if needed.
Inputs & Outputs
Inputs
- File types:
.csv
Outputs
tables/mapped_counts.csvtables/mapping_table.csvtables/unmapped_genes.csvreport.mdresult.json- Produces artifact
bulkrna.count_matrixastables/mapped_counts.csv(csv)
Flow
- Load count matrix.
- Strip Ensembl version suffixes (
bulkrna_geneid_mapping.py:78:ENSG00000141510.12 → ENSG00000141510). - Look up each ID in the built-in mapping table; fall back to the mygene API if available (
:88warns and skips API path ifmygenenot importable). - Resolve duplicate-target collisions per
--on-duplicate(sum/first/drop). - Write
tables/mapped_counts.csv,tables/mapping_table.csv,tables/unmapped_genes.csv.
Gotchas
- mygene API is opt-in via package install, not a CLI flag.
bulkrna_geneid_mapping.py:88falls back silently whenmygeneis not importable, leaving you with built-in-table coverage only. The summary dict does not record whether the API was used; the only signal is the warning log line and thepct_mappedvalue (built-in tables cover ~20 well-known cancer-relevant genes — anything substantially higher implies the API ran). --from/--toonly acceptensembl,entrez,symbol(bulkrna_geneid_mapping.py:271-274). UniProt and other namespaces are not in the choices list and will fail at argparse. If you need UniProt, supply a custom--mapping-fileTSV.- Built-in tables cover human + mouse only (
--specieschoices at:275). Other organisms fail with empty mappings ifmygeneisn't installed; either installmygeneor supply--mapping-file. - Many-to-one collapses follow
--on-duplicate(defaultsum). Default sums read counts across genes mapping to the same target symbol — meaningful for paralog families but wrong if you wanted per-isoform tracking. Choosefirstto take the first hit, ordropto keep only unique mappings. The number resolved is inresult.json["n_duplicates_resolved"]. - Ensembl version stripping is unconditional (
:78). If your downstream tool requires the version suffix (rare), this skill silently drops it.
What ships with it
5 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.
- 10d ago First seen · 88 lines · 59 tokens per session scan A 6d6da726cd76
bulkrna-geneid-mapping is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 59 tokens to every session and 1,096 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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