A guide to statistical workflows for Frites and higher-order interaction analysis. It explains permutation tests, cluster correction, bootstrapping, and fixed- or random-effect inference; these are methods for judging whether patterns in scientific data are likely to be meaningful.

Use it after choosing a Frites or higher-order-interaction tool to understand the workflow, statistical assumptions, and how to apply the results to scientific data.

The underlying analysis tools do not automatically provide all significance testing, so choosing and interpreting the right statistical procedure can be difficult.

workflows — Skill for Claude Code by brainets/braina

Install

Getting it into your agent

This one installs as part of its plugin. Adding the marketplace and installing the plugin brings it with everything else the plugin ships.

Claude Code

/plugin marketplace add brainets/braina

Claude Code

/plugin install braina

Made for: Claude Code.

Or install braina, the plugin that ships this one along with the rest of its 5 skills, 1 hook.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/brainets/braina/workflows/github.svg)](https://agentmods.dev/skills/brainets/braina/workflows)

Your own site

<a href="https://agentmods.dev/skills/brainets/braina/workflows"><img src="https://agentmods.dev/badge/skills/brainets/braina/workflows/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/brainets/braina/workflows"><img src="https://agentmods.dev/badge/skills/brainets/braina/workflows.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 132 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,607 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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	$0.00132	$0.01607
Opus 5.5	$0.00053	$0.00643
Sonnet 5.5	$0.00026	$0.00321
Haiku 4.5	$0.00013	$0.00161

Measured 29d ago against content hash c66e28304ec4, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

workflows 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 29d 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.

plugin/skills/workflows/SKILL.md · 100 lines

How it starts

The opening of the file, as written. The whole thing — 100 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Statistical workflows for Frites and HOI

Covers the four workflow tools - frites_wf_stats, frites_wf_mi, frites_wf_conn_comod, frites_wf_mi_combine - and how the same permutation machinery applies to HOI output. How the test works internally (null construction, rfx t-test, cluster correction) is in references/permutation-internals.md next to this file; read it when the question is "why" rather than "which parameter".

Neither the bare frites_conn_* tools nor the hoi_* tools compute significance. frites_wf_stats is a generic non-parametric engine: it only needs an effect and a matching permutation null, whatever produced them.

`frites_wf_stats` - statistics on a precomputed effect

Inputs: effect (n_roi, n_subjects, n_times) and permutations (n_perm, n_roi, n_subjects, n_times) (.npy or .nc; a .nc with roi/times coordinates gives labelled outputs). "roi" may be any unit of test: pairs, multiplets, frequencies.
inference (rfx | ffx), mcp (cluster | maxstat | fdr | bonferroni), tail (-1, 0, 1), cluster_th (None = auto).
Writes <prefix>_pvalues.nc and, for rfx, <prefix>_tvalues.nc, both (times, roi).
Not exposed: cluster_alpha, ttested, rfx_sigma, rfx_center (library defaults 0.05, False, 0.001, False). API: https://brainets.github.io/frites/api/generated/frites.workflow.WfStats.html

`frites_wf_mi` - MI about y with built-in statistics

Data: one file per subject (data_path=[...], y_path=[...]) or a .nc with a subject dimension; single file = single subject. rfx requires at least two subjects (refused otherwise, as Frites asserts).
mi_type: cc continuous y, cd categorical y, ccd conditional (y continuous, z categorical - z not exposed via MCP).
inference, n_perm, mcp (cluster default; maxstat, fdr, bonferroni, nostat), cluster_th (None auto or 'tfce'), cluster_alpha, random_state (reproducible permutations), estimator (default GCMI, or pearson/spearman/dcorr/binmi for cc), n_jobs.
save_workflow=True pickles the fitted workflow to <prefix>_wf.pkl for frites_wf_mi_combine.
Outputs <prefix>_mi.nc and <prefix>_pvalues.nc, (times, roi). API: https://brainets.github.io/frites/api/generated/frites.workflow.WfMi.html

Read the full file on GitHub · 100 lines

Files

What ships with it

1 file 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.

references/permutation-internals.md 2.6 KB

Changes

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.

29d ago Changed · -91 lines · +12 tokens per session c66e28304ec4
1mo ago First seen · 191 lines · 120 tokens per session scan A db271b476045

Subscribe to this mod's changes

workflows is a skill published in the GitHub repository brainets/braina (5 stars, last pushed 1mo ago), licensed BSD-3-Clause. It adds 132 tokens to every session and 1,607 once invoked, about $0.0005 per session on Opus 5.5. 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 2026-09-14.

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