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 sc-consensus-pseudotimegit 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/sc-consensus-pseudotime)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-consensus-pseudotime"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-consensus-pseudotime.svg" alt="Measured on agentmods" height="20"></a>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 | $0.00074 | $0.01023 |
| Opus 5 | $0.00037 | $0.00511 |
| Sonnet 5 | $0.00015 | $0.00205 |
| Haiku 4.5 | $0.00007 | $0.00102 |
Grade A, and why
sc-consensus-pseudotime 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 3d 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 — 101 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sc-consensus-pseudotime
When to use
Verified continuous consensus over pseudotime methods (ADR 0031). A single
pseudotime is sensitive to which algorithm produced it: DPT, Palantir and VIA make
different assumptions and can order cells differently. Use this when you have a
preprocessed single-cell AnnData and a defined root (a --root-cluster or
--root-cell) and want a pseudotime that is not an artifact of one method, with
a per-cell uncertainty band.
A pseudotime is only defined up to a monotone reparameterisation and a direction
flip, so the runtime makes members comparable by rank-normalisation (cancels the
monotone gauge) + a direction safeguard (anchored flip), then aggregates a
consensus by per-cell median (default) or agreement-weighted mean, re-ranked to
[0, 1]. v1 is agreement-only (scored by mean pairwise Spearman).
Inputs & Outputs
Inputs
- Modalities: scrna
- File types:
.h5ad - Requires a preprocessed AnnData (
Xnormalised, PCA/neighbours present)
Outputs
consensus_pseudotime.tsvmember_agreement_spearman.csvmember_scores.csvselection_audit.jsonplan.jsonreport.md
Flow
- Plan one member per pseudotime method, all sharing the user's root.
- Fan out
sc-pseudotime --method <m>and gather each member's canonicalobs['pseudotime']. - Rank-normalise + direction-align; drop any degenerate (constant) member.
- Score members by mean pairwise Spearman; select the top-K.
- Aggregate via
median/weighted, re-rank to[0, 1], and report per-cell dispersion + a weak-agreement guard.
Gotchas
- A shared root is required — without
--root-cluster/--root-cellthe run aborts (the root pins pseudotime direction so the consensus is well-posed). - v1 members are single-global-pseudotime methods (dpt/palantir/via); multi-lineage methods (slingshot/monocle3/cellrank) are deferred — they re-introduce branching topology, which is out of scope.
- A weak-agreement warning (mean Spearman < 0.5) means the methods disagree on the ordering: the data may have no single shared trajectory. It is reported, not fatal.
pseudotime_madis a majority-support metric; read the per-cellrangealongside it to catch a lone strongly-disagreeing method.
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.
- 3d ago First seen · 101 lines · 74 tokens per session scan A 674e539f19f4
sc-consensus-pseudotime is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 74 tokens to every session and 1,023 once invoked, about $0.0004 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 2026-09-03.
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